Variant report

Variant	rs6798243
Chromosome Location	chr3:195098532-195098533
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:195097533..195099212-chr3:195100181..195102038,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11919965	1.00[CHB][hapmap]
rs12485302	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12485380	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12485407	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12485433	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12485787	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12486168	1.00[CHB][hapmap]
rs12486220	1.00[CHB][hapmap]
rs12486241	0.83[AMR][1000 genomes]
rs12486536	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12486636	1.00[CHB][hapmap]
rs12486805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12486835	1.00[CHB][hapmap]
rs12487670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487961	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12488451	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12488481	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12488562	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12488616	1.00[CHB][hapmap]
rs12488869	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12489090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489620	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489849	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12490460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs12490658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12491026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12491371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12491581	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12491670	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12491736	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12491788	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12491808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs12491854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs12492552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12494564	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12494759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12494773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12494820	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12494883	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12495657	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12496202	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12496204	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12496885	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497178	0.83[AMR][1000 genomes]
rs12497478	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12497671	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497677	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497906	1.00[CHB][hapmap]
rs1808074	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2029707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs2050807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2050808	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2410840	0.90[YRI][hapmap]
rs34643420	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35419807	0.83[AMR][1000 genomes]
rs3773419	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3773420	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3796161	1.00[CHB][hapmap]
rs41266981	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41266999	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41267003	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56211708	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59535864	0.95[AFR][1000 genomes]
rs60040536	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6767801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6777904	1.00[CHB][hapmap]
rs6804467	1.00[CHB][hapmap]
rs72499627	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607893	0.81[AMR][1000 genomes]
rs72607894	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72607895	0.86[AMR][1000 genomes]
rs72607896	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72607897	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72607898	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72607899	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72607900	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72607901	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72607902	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72611103	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73080808	1.00[AFR][1000 genomes]
rs73080815	0.91[AFR][1000 genomes]
rs755202	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs7642127	1.00[CHB][hapmap]
rs7653179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs999331	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
3	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
4	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
5	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
8	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
9	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
10	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
11	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
12	nsv432512	chr3:195007260-195475989	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
13	nsv526569	chr3:195038287-195123495	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
14	nsv878138	chr3:195057001-195477791	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
15	nsv878139	chr3:195058837-195158031	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	esv1799680	chr3:195060129-195154361	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
17	nsv878141	chr3:195065255-195158031	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1006229	chr3:195071421-195474751	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195040400-195108400	Weak transcription	Colonic Mucosa	Colon
2	chr3:195040600-195111200	Weak transcription	Fetal Brain Male	brain
3	chr3:195041000-195131200	Weak transcription	Gastric	stomach
4	chr3:195049600-195106000	Weak transcription	HUVEC	blood vessel
5	chr3:195052200-195102800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:195052400-195118000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:195061600-195101800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:195062600-195102000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:195065000-195114800	Weak transcription	Osteobl	bone
10	chr3:195074200-195113200	Weak transcription	HSMMtube	muscle
11	chr3:195074400-195100200	Weak transcription	HSMM	muscle
12	chr3:195074800-195118000	Weak transcription	K562	blood
13	chr3:195077000-195105800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:195077400-195118000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:195077800-195114200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:195077800-195117800	Weak transcription	Brain Angular Gyrus	brain
17	chr3:195077800-195122800	Weak transcription	Right Ventricle	heart
18	chr3:195078000-195100400	Weak transcription	Brain Anterior Caudate	brain
19	chr3:195078000-195101200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:195078000-195101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:195078000-195103400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:195078000-195106200	Weak transcription	Brain Substantia Nigra	brain
23	chr3:195078000-195110600	Weak transcription	Left Ventricle	heart
24	chr3:195078000-195142200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:195078200-195101600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:195078400-195100200	Weak transcription	Dnd41	blood
27	chr3:195078400-195106200	Weak transcription	Fetal Heart	heart
28	chr3:195078400-195107200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:195078400-195107200	Weak transcription	Esophagus	oesophagus
30	chr3:195078400-195111000	Weak transcription	Fetal Brain Female	brain
31	chr3:195078600-195118000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:195079000-195106200	Weak transcription	Fetal Kidney	kidney
33	chr3:195079800-195114400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:195081200-195101800	Weak transcription	GM12878-XiMat	blood
35	chr3:195084200-195108800	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:195085800-195102000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:195087000-195101600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:195087200-195101600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:195087200-195104000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:195087400-195109000	Weak transcription	Pancreas	Pancrea
41	chr3:195087600-195102000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:195087800-195101600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:195087800-195131200	Weak transcription	NHDF-Ad	bronchial
44	chr3:195088200-195115200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:195088400-195111200	Weak transcription	NH-A	brain
46	chr3:195088600-195146800	Weak transcription	Spleen	Spleen
47	chr3:195090000-195098600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr3:195090800-195116800	Weak transcription	Aorta	Aorta
49	chr3:195091000-195100400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:195091000-195101400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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