Variant report

Variant	rs17080289
Chromosome Location	chr3:48643891-48643892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48638279..48640259-chr3:48642754..48644791,3	MCF-7	breast:
2	chr3:48338306..48341103-chr3:48643663..48646394,2	K562	blood:
3	chr3:48641673..48644998-chr3:48670911..48673807,4	K562	blood:
4	chr3:48643318..48645059-chr3:48645193..48646900,2	MCF-7	breast:
5	chr3:48639116..48644270-chr3:48645185..48648761,6	K562	blood:
6	chr3:48640950..48644386-chr3:48644481..48647187,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225697	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000172113	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1003649	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap]
rs10470687	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.83[ASN][1000 genomes]
rs11706983	1.00[GIH][hapmap]
rs11708786	1.00[GIH][hapmap]
rs11713694	0.83[GIH][hapmap]
rs11719291	1.00[GIH][hapmap]
rs12107252	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs12107418	1.00[GIH][hapmap]
rs13060933	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13063312	0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs13070798	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs13074318	0.83[GIH][hapmap]
rs13091944	0.90[CHB][hapmap];0.89[YRI][hapmap]
rs13319635	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13319651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13324142	0.90[CHD][hapmap];1.00[GIH][hapmap]
rs13434258	1.00[GIH][hapmap]
rs2006871	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs2255532	0.82[CHB][hapmap]
rs2276850	0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs2276852	0.85[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs2286652	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs2310996	0.90[CHD][hapmap];1.00[GIH][hapmap];0.84[ASN][1000 genomes]
rs2854394	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2854395	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28581474	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34037363	0.83[GIH][hapmap]
rs34107861	0.80[CHD][hapmap]
rs34368826	0.81[ASN][1000 genomes]
rs35064573	1.00[GIH][hapmap]
rs35343040	0.98[ASN][1000 genomes]
rs35562294	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35796820	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755819	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3806694	0.81[ASN][1000 genomes]
rs3821876	0.90[CHD][hapmap];1.00[GIH][hapmap]
rs3969942	0.85[CHD][hapmap];0.83[GIH][hapmap]
rs57334642	0.81[ASN][1000 genomes]
rs6781283	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6792156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[ASN][1000 genomes]
rs6792525	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.83[ASN][1000 genomes]
rs6806059	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap]
rs740787	0.90[CHD][hapmap];1.00[GIH][hapmap];0.84[ASN][1000 genomes]
rs7620853	0.84[ASN][1000 genomes]
rs7631574	0.90[CHD][hapmap];1.00[GIH][hapmap];0.84[ASN][1000 genomes]
rs9810549	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9810991	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9811318	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs9812200	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs9814951	0.80[CHB][hapmap]
rs9830581	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9836462	0.85[CHD][hapmap];1.00[GIH][hapmap]
rs9837687	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap]
rs9841602	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs9843316	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850102	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap]
rs9851771	0.83[GIH][hapmap]
rs9868809	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs9869698	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap]
rs9871180	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9875911	0.83[GIH][hapmap]
rs9878063	0.81[ASN][1000 genomes]
rs9878950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.85[ASN][1000 genomes]
rs9881877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]
rs9882549	1.00[GIH][hapmap]
rs9882962	0.81[CHD][hapmap];0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48634200-48644200	Strong transcription	Brain Germinal Matrix	brain
2	chr3:48634200-48644600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:48634200-48646200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:48634600-48644000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:48634600-48644400	Strong transcription	Primary T cells from cord blood	blood
6	chr3:48634600-48645200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:48634600-48645200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:48634600-48645600	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr3:48634600-48645600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:48634600-48645600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:48634600-48645800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:48634800-48644000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:48634800-48644000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:48634800-48645600	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr3:48634800-48645600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:48634800-48645600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:48635000-48644000	Strong transcription	Dnd41	blood
18	chr3:48635000-48644400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:48635000-48644400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:48635000-48645600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:48635000-48645600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:48635000-48645600	Strong transcription	Fetal Intestine Large	intestine
23	chr3:48635200-48644000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:48635400-48644000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:48635400-48644000	Strong transcription	Brain Cingulate Gyrus	brain
26	chr3:48635600-48645600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:48636200-48645400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:48636400-48644000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:48636400-48645400	Strong transcription	Brain Angular Gyrus	brain
30	chr3:48636400-48645400	Strong transcription	Fetal Intestine Small	intestine
31	chr3:48636600-48644000	Strong transcription	K562	blood
32	chr3:48637200-48644000	Strong transcription	Fetal Lung	lung
33	chr3:48637200-48644000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr3:48637200-48645400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:48637200-48645600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr3:48637400-48645000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:48637400-48645600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:48637400-48645600	Strong transcription	Fetal Muscle Leg	muscle
39	chr3:48637400-48645600	Strong transcription	Fetal Stomach	stomach
40	chr3:48637600-48644400	Strong transcription	Osteobl	bone
41	chr3:48637600-48645200	Strong transcription	NHLF	lung
42	chr3:48637600-48645400	Strong transcription	Placenta	Placenta
43	chr3:48637800-48644400	Strong transcription	NH-A	brain
44	chr3:48637800-48645400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:48637800-48645600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:48637800-48645800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:48638000-48645400	Strong transcription	Fetal Thymus	thymus
48	chr3:48638000-48645600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr3:48638200-48645200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:48638400-48645000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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