Variant report

Variant	rs7616634
Chromosome Location	chr3:100109150-100109151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100107041..100109680-chr3:100110808..100112599,2	MCF-7	breast:
2	chr3:100104411..100107248-chr3:100108549..100110661,2	MCF-7	breast:
3	chr3:100107045..100110476-chr3:100114433..100116956,3	MCF-7	breast:
4	chr3:100107521..100109906-chr3:100428275..100429985,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114354	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10936180	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1123578	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1214380	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1214381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1228184	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1530283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs166747	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277622	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277623	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277626	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277628	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277629	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277630	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277638	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277639	0.82[MEX][hapmap]
rs277641	0.82[MEX][hapmap]
rs277642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277644	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277651	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs372438	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772692	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs392066	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs402870	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs413425	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431069	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs432715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6780662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs6791102	0.92[ASN][1000 genomes]
rs6794955	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641630	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100087600-100114600	Weak transcription	Small Intestine	intestine
2	chr3:100090200-100118400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:100091600-100117600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:100096800-100109800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:100096800-100112800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:100099000-100110200	Weak transcription	Spleen	Spleen
7	chr3:100099000-100118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:100099800-100117600	Weak transcription	Colonic Mucosa	Colon
9	chr3:100100800-100110800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:100102800-100118200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:100103800-100112800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:100103800-100117600	Weak transcription	Fetal Kidney	kidney
13	chr3:100103800-100118600	Weak transcription	Brain Substantia Nigra	brain
14	chr3:100104000-100117600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:100104200-100114600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:100104200-100117600	Weak transcription	Brain Angular Gyrus	brain
17	chr3:100104200-100117600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:100104200-100117600	Weak transcription	Psoas Muscle	Psoas
19	chr3:100104200-100117600	Weak transcription	Thymus	Thymus
20	chr3:100104200-100117800	Weak transcription	Esophagus	oesophagus
21	chr3:100104200-100118200	Weak transcription	HSMMtube	muscle
22	chr3:100104200-100118600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:100104200-100118600	Weak transcription	Aorta	Aorta
24	chr3:100104400-100110800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:100104400-100117200	Weak transcription	NHEK	skin
26	chr3:100104600-100117600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:100104600-100117600	Weak transcription	Fetal Brain Male	brain
28	chr3:100104600-100118600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:100104800-100117400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:100105000-100115800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:100105200-100117600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:100105200-100118400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:100105200-100118600	Weak transcription	Placenta	Placenta
34	chr3:100105400-100112600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:100105600-100114600	Weak transcription	Hela-S3	cervix
36	chr3:100105800-100109400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:100105800-100112800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:100105800-100114400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:100105800-100118200	Weak transcription	HMEC	breast
40	chr3:100106000-100110800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:100106000-100117600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:100106000-100117800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:100106200-100115400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:100106200-100117400	Weak transcription	Osteobl	bone
45	chr3:100106200-100117800	Weak transcription	NH-A	brain
46	chr3:100106200-100118200	Weak transcription	HUVEC	blood vessel
47	chr3:100106400-100115800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:100106400-100116800	Weak transcription	Left Ventricle	heart
49	chr3:100106400-100117400	Weak transcription	Fetal Heart	heart
50	chr3:100106400-100117800	Weak transcription	Lung	lung

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