Variant report

Variant	rs9892425
Chromosome Location	chr17:57241938-57241939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:57234006..57238317-chr17:57241517..57243388,3	MCF-7	breast:
2	chr17:57234047..57238227-chr17:57239348..57243138,5	MCF-7	breast:
3	chr17:57237065..57238578-chr17:57239963..57242337,2	K562	blood:
4	chr17:57241782..57244685-chr17:57694052..57697026,3	MCF-7	breast:
5	chr17:57230437..57234042-chr17:57239910..57246208,6	MCF-7	breast:
6	chr17:57232913..57236116-chr17:57239263..57243246,3	K562	blood:

Variant related genes	Relation type
ENSG00000182628	Chromatin interaction
ENSG00000068489	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11654986	0.86[YRI][hapmap]
rs12051896	0.82[ASN][1000 genomes]
rs12051897	0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs12603238	0.86[YRI][hapmap]
rs12948746	0.86[YRI][hapmap]
rs35448939	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4932693	0.86[YRI][hapmap]
rs62081890	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62081892	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6503893	0.86[YRI][hapmap]
rs6503898	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7208505	0.86[YRI][hapmap]
rs7213269	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7214098	0.86[YRI][hapmap]
rs7217845	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7223587	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7342863	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.94[MKK][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7502541	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7502947	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs7503190	0.86[YRI][hapmap]
rs8067264	0.86[YRI][hapmap]
rs8067682	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.94[MKK][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8069033	0.87[YRI][hapmap]
rs8072182	0.87[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8073316	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8073699	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8077052	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8081967	0.86[YRI][hapmap]
rs8082544	0.86[YRI][hapmap]
rs9303403	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9909925	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.94[MKK][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9910629	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9911583	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9915267	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv908643	chr17:56803028-57249010	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
2	nsv908644	chr17:56803028-57371432	Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
3	esv3335958	chr17:56849544-57385398	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	nsv1065063	chr17:56954121-57346694	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
5	nsv1064384	chr17:57049519-57346694	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
6	nsv908646	chr17:57061238-57255810	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv833499	chr17:57070693-57288410	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	208 gene(s)	inside rSNPs	diseases
8	nsv1066388	chr17:57082013-57339981	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	209 gene(s)	inside rSNPs	diseases
9	esv2758462	chr17:57082579-57425634	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	213 gene(s)	inside rSNPs	diseases
10	esv2758699	chr17:57082579-57425634	Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	213 gene(s)	inside rSNPs	diseases
11	nsv1066467	chr17:57117682-57338731	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	200 gene(s)	inside rSNPs	diseases
12	nsv1057209	chr17:57117682-57742240	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
13	nsv543396	chr17:57117682-57742240	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
14	nsv1066788	chr17:57126446-57344129	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	193 gene(s)	inside rSNPs	diseases
15	nsv482858	chr17:57136446-57288615	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	184 gene(s)	inside rSNPs	diseases
16	nsv908647	chr17:57165097-57290383	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
17	nsv908648	chr17:57165097-57322954	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	179 gene(s)	inside rSNPs	diseases
18	nsv1063542	chr17:57179669-57569673	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
19	nsv543397	chr17:57179669-57569673	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
20	nsv1062959	chr17:57179669-57680772	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
21	nsv1060807	chr17:57189467-57344129	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	114 gene(s)	inside rSNPs	diseases
22	nsv1064115	chr17:57199370-57369270	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
23	nsv575802	chr17:57208752-57344181	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
24	nsv917030	chr17:57229066-57624963	Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
25	nsv534343	chr17:57229181-57624852	Active TSS Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
26	nsv1065442	chr17:57235466-57324970	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
27	nsv1057152	chr17:57235466-57627246	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
28	nsv1058166	chr17:57237263-57501803	Bivalent/Poised TSS Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
29	nsv1065619	chr17:57237263-57783629	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
30	nsv543398	chr17:57237263-57783629	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9892425	RAD51C	cis	Adipose Subcutaneous	GTEx
rs9892425	RAD51C	cis	Esophagus Mucosa	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:57233600-57243400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr17:57233800-57243400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:57233800-57287000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:57234000-57243200	Weak transcription	Fetal Brain Female	brain
5	chr17:57234000-57243400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr17:57234000-57243400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr17:57234000-57243600	Weak transcription	Fetal Lung	lung
8	chr17:57234000-57247000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr17:57234000-57248200	Weak transcription	Fetal Muscle Leg	muscle
10	chr17:57234200-57243400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr17:57234200-57248000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr17:57234400-57243200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr17:57234400-57244600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:57234400-57247400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr17:57234400-57247400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr17:57234400-57249600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr17:57234400-57262400	Weak transcription	HSMM	muscle
18	chr17:57234600-57243200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr17:57234600-57243200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr17:57234600-57243200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr17:57234600-57243400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr17:57234600-57249400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr17:57234800-57242800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr17:57235200-57243200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr17:57235200-57250000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr17:57235400-57243400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr17:57235400-57249400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr17:57235400-57249400	Weak transcription	Brain Germinal Matrix	brain
29	chr17:57235600-57243400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr17:57235800-57244800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr17:57237000-57243200	Weak transcription	Fetal Heart	heart
32	chr17:57237000-57243200	Weak transcription	NH-A	brain
33	chr17:57237200-57243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:57237200-57243200	Weak transcription	Hela-S3	cervix
35	chr17:57237400-57243400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr17:57237600-57243000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr17:57237800-57243000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr17:57237800-57243200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr17:57237800-57243200	Weak transcription	HMEC	breast
40	chr17:57237800-57243200	Weak transcription	NHEK	skin
41	chr17:57238000-57242600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr17:57238000-57243200	Weak transcription	A549	lung
43	chr17:57238000-57243400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr17:57238000-57245000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr17:57238200-57243400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr17:57238200-57243400	Weak transcription	NHLF	lung
47	chr17:57238200-57276600	Weak transcription	Primary T cells from cord blood	blood
48	chr17:57238400-57243400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr17:57238400-57243400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr17:57238400-57243400	Weak transcription	Stomach Mucosa	stomach

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