Variant report

Variant	rs3099419
Chromosome Location	chr8:95556959-95556960
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:95556183..95559262-chr8:95651441..95653267,3	MCF-7	breast:
2	chr8:95429301..95430964-chr8:95556337..95558310,2	MCF-7	breast:
3	chr8:95554974..95557880-chr8:95564950..95566849,3	MCF-7	breast:
4	chr8:95555945..95557652-chr8:95557953..95559866,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212997	Chromatin interaction
ENSG00000164944	Chromatin interaction
ENSG00000261437	Chromatin interaction
ENSG00000253704	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11991172	0.87[AFR][1000 genomes]
rs1866844	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs2304765	0.89[YRI][hapmap]
rs2450579	0.85[GIH][hapmap];0.86[MEX][hapmap]
rs2470736	0.95[GIH][hapmap];0.86[MEX][hapmap]
rs2470737	0.95[GIH][hapmap]
rs2470743	0.95[GIH][hapmap]
rs3096602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096605	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs3098711	0.88[YRI][hapmap]
rs3098713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098717	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3098720	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3098721	0.85[YRI][hapmap]
rs3098723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3098724	0.85[ASW][hapmap];0.81[CHB][hapmap];0.89[YRI][hapmap]
rs3098726	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3099402	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3099408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099409	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3099411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099415	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3099416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3099417	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3099418	0.82[YRI][hapmap]
rs3099421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099423	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3099424	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3102843	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3102844	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3102849	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3102858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102863	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3102864	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3102866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3102868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3102869	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3102870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3102871	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102872	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102873	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102876	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3133597	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3133598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3133599	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3133606	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3133607	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3133612	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3133614	0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap]
rs3133623	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs3133624	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs3133638	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3133642	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3133643	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3133644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[ASN][1000 genomes]
rs3133646	0.85[YRI][hapmap]
rs3133647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3133650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3133652	1.00[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3133653	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3133659	0.82[YRI][hapmap]
rs3133661	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34432191	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36040483	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs882521	0.95[GIH][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv429928	chr8:95488800-95672033	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv611750	chr8:95519205-95574634	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers 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	13 gene(s)	inside rSNPs	diseases
6	nsv1017256	chr8:95555083-95570079	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1026768	chr8:95556054-95569566	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1033318	chr8:95556054-95576338	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1032065	chr8:95556054-95578349	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1016339	chr8:95556054-95585807	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1021702	chr8:95556054-95589194	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv1033345	chr8:95556375-95570533	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers 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	9 gene(s)	inside rSNPs	diseases
13	nsv1029802	chr8:95556959-95578349	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95497200-95564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr8:95532800-95558800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr8:95536600-95557000	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr8:95537000-95557400	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr8:95537000-95558600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr8:95541600-95563600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr8:95541600-95563800	Weak transcription	Stomach Mucosa	stomach
8	chr8:95543200-95563200	Weak transcription	Fetal Brain Male	brain
9	chr8:95543200-95564800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr8:95543200-95564800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr8:95543600-95558000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr8:95543600-95564000	Weak transcription	HSMMtube	muscle
13	chr8:95544400-95558000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr8:95545200-95564000	Weak transcription	Psoas Muscle	Psoas
15	chr8:95546200-95564800	Weak transcription	Esophagus	oesophagus
16	chr8:95546400-95564000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr8:95546400-95564000	Weak transcription	Aorta	Aorta
18	chr8:95546600-95563600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr8:95546800-95558400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr8:95546800-95563600	Weak transcription	Brain Angular Gyrus	brain
21	chr8:95547000-95563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr8:95547000-95564000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr8:95547000-95565000	Weak transcription	Pancreas	Pancrea
24	chr8:95547200-95563200	Weak transcription	Gastric	stomach
25	chr8:95547400-95563200	Weak transcription	Brain Substantia Nigra	brain
26	chr8:95547400-95563600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr8:95548000-95563600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr8:95548400-95563800	Weak transcription	Brain Hippocampus Middle	brain
29	chr8:95548400-95563800	Weak transcription	Small Intestine	intestine
30	chr8:95548800-95564000	Weak transcription	Colonic Mucosa	Colon
31	chr8:95549000-95558800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr8:95549000-95563000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr8:95549000-95563800	Weak transcription	HUVEC	blood vessel
34	chr8:95549000-95564000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr8:95549000-95564000	Weak transcription	Brain Germinal Matrix	brain
36	chr8:95549400-95561800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr8:95549400-95563200	Weak transcription	Ovary	ovary
38	chr8:95549400-95563400	Weak transcription	NHDF-Ad	bronchial
39	chr8:95549400-95564000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr8:95549600-95563800	Weak transcription	Brain Anterior Caudate	brain
41	chr8:95550000-95563600	Weak transcription	NH-A	brain
42	chr8:95550400-95563200	Weak transcription	Fetal Brain Female	brain
43	chr8:95550600-95564000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr8:95550600-95564400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr8:95551600-95564800	Weak transcription	Thymus	Thymus
46	chr8:95552000-95563600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr8:95552200-95561000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr8:95552200-95561000	Weak transcription	Left Ventricle	heart
49	chr8:95552200-95561200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr8:95552200-95562000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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