Variant report

Variant	rs9911583
Chromosome Location	chr17:57210721-57210722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:57186315..57188698-chr17:57208953..57211080,2	MCF-7	breast:
2	chr17:57200028..57201874-chr17:57209514..57212226,2	MCF-7	breast:
3	chr17:57183248..57185852-chr17:57209111..57211158,2	MCF-7	breast:
4	chr17:57209257..57211586-chr17:57216114..57217876,2	K562	blood:

Variant related genes	Relation type
ENSG00000108395	Chromatin interaction
ENSG00000224738	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11654986	0.86[YRI][hapmap]
rs12051896	0.89[ASN][1000 genomes]
rs12051897	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs12603238	0.86[YRI][hapmap]
rs12948746	0.86[YRI][hapmap]
rs4932693	0.86[YRI][hapmap]
rs62081890	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62081892	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6503893	0.86[YRI][hapmap]
rs6503898	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7208505	0.86[YRI][hapmap]
rs7213269	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7214098	0.86[YRI][hapmap]
rs7217845	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7223587	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7342863	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7502541	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7502947	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7503190	0.86[YRI][hapmap]
rs8067264	0.86[YRI][hapmap]
rs8067682	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8069033	0.86[YRI][hapmap]
rs8072182	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073316	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8073699	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8077052	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8081967	0.86[YRI][hapmap]
rs8082544	0.86[YRI][hapmap]
rs9303403	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9892425	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]
rs9909925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9910629	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915267	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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	esv1792828	chr17:57185807-57219391	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
22	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
23	esv2761969	chr17:57192821-57211602	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
24	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
25	esv1803083	chr17:57206124-57233048	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	87 gene(s)	inside rSNPs	diseases
26	esv1793348	chr17:57207540-57233048	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	87 gene(s)	inside rSNPs	diseases
27	esv1800539	chr17:57208752-57233048	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	87 gene(s)	inside rSNPs	diseases
28	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9911583	MTMR4	cis	lymphoblastoid	seeQTL
rs9911583	SUPT4H1	cis	cerebellum	SCAN
rs9911583	SUPT4H1	cis	parietal	SCAN
rs9911583	RAD51C	cis	multi-tissue	Pritchard
rs9911583	BZRAP1	cis	cerebellum	SCAN
rs9911583	F2RL1	trans	cerebellum	SCAN
rs9911583	RAD51C	cis	Adipose Subcutaneous	GTEx
rs9911583	RAD51C	cis	parietal	SCAN
rs9911583	RAD51C	cis	lymphoblastoid	seeQTL
rs9911583	RAD51C	cis	Esophagus Mucosa	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:57184800-57231000	Weak transcription	Aorta	Aorta
2	chr17:57185000-57211200	Weak transcription	Right Ventricle	heart
3	chr17:57185000-57212000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:57185000-57218800	Weak transcription	Fetal Intestine Large	intestine
5	chr17:57185000-57221600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:57185000-57231000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr17:57185000-57231200	Weak transcription	Lung	lung
8	chr17:57185200-57212800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr17:57185200-57223000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:57185200-57226200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr17:57185200-57228400	Weak transcription	Fetal Heart	heart
12	chr17:57185600-57227800	Weak transcription	Fetal Brain Male	brain
13	chr17:57186000-57231200	Weak transcription	Colon Smooth Muscle	Colon
14	chr17:57189200-57230400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr17:57192200-57212000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:57192400-57229600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr17:57193200-57215800	Weak transcription	NHEK	skin
18	chr17:57193200-57219800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr17:57193600-57223200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr17:57194400-57231200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:57195600-57230400	Weak transcription	Fetal Intestine Small	intestine
22	chr17:57196600-57226000	Weak transcription	HUVEC	blood vessel
23	chr17:57196600-57226600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:57196800-57226600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr17:57197600-57228400	Weak transcription	Fetal Brain Female	brain
26	chr17:57198000-57231000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr17:57198200-57230800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr17:57198800-57231000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr17:57199800-57216800	Weak transcription	HMEC	breast
30	chr17:57200200-57229200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr17:57202200-57220600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr17:57202200-57226000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr17:57202400-57227200	Weak transcription	Left Ventricle	heart
34	chr17:57203000-57225800	Weak transcription	NHLF	lung
35	chr17:57203000-57227200	Weak transcription	Small Intestine	intestine
36	chr17:57204000-57222800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:57204200-57219200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr17:57204600-57221600	Weak transcription	Hela-S3	cervix
39	chr17:57204600-57226400	Weak transcription	GM12878-XiMat	blood
40	chr17:57204800-57211600	Weak transcription	Adipose Nuclei	Adipose
41	chr17:57204800-57226600	Weak transcription	HSMM	muscle
42	chr17:57205200-57216000	Weak transcription	Placenta	Placenta
43	chr17:57205200-57225800	Weak transcription	NHDF-Ad	bronchial
44	chr17:57205200-57229600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr17:57205400-57226000	Weak transcription	Ovary	ovary
46	chr17:57205400-57227200	Weak transcription	Fetal Lung	lung
47	chr17:57205800-57221000	Weak transcription	Brain Germinal Matrix	brain
48	chr17:57205800-57227200	Weak transcription	Primary B cells from cord blood	blood
49	chr17:57205800-57230800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr17:57206000-57220800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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