Variant report

Variant	rs12490460
Chromosome Location	chr3:195159198-195159199
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	chr3:195151499..195154250-chr3:195155188..195159496,5	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11919965	1.00[CHB][hapmap]
rs12485302	0.90[AMR][1000 genomes]
rs12485380	0.86[AMR][1000 genomes]
rs12485407	0.86[AMR][1000 genomes]
rs12485433	0.90[AMR][1000 genomes]
rs12485787	0.86[AMR][1000 genomes]
rs12486168	1.00[CHB][hapmap]
rs12486220	1.00[CHB][hapmap]
rs12486241	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12486536	0.86[AMR][1000 genomes]
rs12486805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs12486835	1.00[CHB][hapmap]
rs12487670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs12487961	0.86[AMR][1000 genomes]
rs12488451	0.93[AMR][1000 genomes]
rs12488481	0.93[AMR][1000 genomes]
rs12488562	0.90[AMR][1000 genomes]
rs12488869	0.86[AMR][1000 genomes]
rs12488979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs12489090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs12489620	0.86[AMR][1000 genomes]
rs12489849	0.93[AMR][1000 genomes]
rs12490658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes]
rs12491026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs12491371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs12491581	0.90[AMR][1000 genomes]
rs12491670	0.93[AMR][1000 genomes]
rs12491736	0.93[AMR][1000 genomes]
rs12491788	0.86[AMR][1000 genomes]
rs12491808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs12494564	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs12494759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs12494773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][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];0.90[AMR][1000 genomes]
rs12494883	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12495657	0.93[AMR][1000 genomes]
rs12496202	0.90[AMR][1000 genomes]
rs12496204	0.93[AMR][1000 genomes]
rs12496885	0.86[AMR][1000 genomes]
rs12497178	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12497478	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs12497671	0.86[AMR][1000 genomes]
rs12497677	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1808074	0.90[AMR][1000 genomes]
rs2029707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs2050808	0.93[AMR][1000 genomes]
rs34643420	0.93[AMR][1000 genomes]
rs35419807	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3773419	0.90[AMR][1000 genomes]
rs3773420	0.90[AMR][1000 genomes]
rs41266981	0.86[AMR][1000 genomes]
rs41266999	0.93[AMR][1000 genomes]
rs41267003	0.93[AMR][1000 genomes]
rs56211708	0.90[AMR][1000 genomes]
rs60040536	0.90[AMR][1000 genomes]
rs6767801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes]
rs6798243	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]
rs6804467	1.00[CHB][hapmap]
rs72499627	0.86[AMR][1000 genomes]
rs72607893	0.84[AMR][1000 genomes]
rs72607894	0.90[AMR][1000 genomes]
rs72607895	0.90[AMR][1000 genomes]
rs72607896	0.90[AMR][1000 genomes]
rs72607897	0.90[AMR][1000 genomes]
rs72607898	0.90[AMR][1000 genomes]
rs72607899	0.90[AMR][1000 genomes]
rs72607900	0.90[AMR][1000 genomes]
rs72607901	0.90[AMR][1000 genomes]
rs72607902	0.90[AMR][1000 genomes]
rs72611103	0.90[AMR][1000 genomes]
rs73890832	0.88[ASN][1000 genomes]
rs73890833	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs755202	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs7642127	1.00[CHB][hapmap]
rs7653179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	esv2754364	chr3:195102703-195553690	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription 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	54 gene(s)	inside rSNPs	diseases
13	esv2757028	chr3:195102787-195479748	Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
14	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats 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	144 gene(s)	inside rSNPs	diseases
15	nsv432513	chr3:195121072-195478861	Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
16	nsv432514	chr3:195121110-195478861	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
17	nsv432515	chr3:195121110-195528226	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
18	nsv829824	chr3:195131067-195286698	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12490460	FAM43A	cis	lymphoblastoid	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195094800-195161200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:195095200-195161800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:195131800-195160600	Weak transcription	Hela-S3	cervix
4	chr3:195132000-195161200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:195133800-195161000	Weak transcription	NHDF-Ad	bronchial
6	chr3:195144800-195161200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:195145600-195162400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:195147000-195161000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:195147000-195162200	Weak transcription	Esophagus	oesophagus
10	chr3:195147200-195161800	Weak transcription	Fetal Thymus	thymus
11	chr3:195147800-195159200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:195147800-195160400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:195147800-195162400	Weak transcription	Left Ventricle	heart
14	chr3:195148000-195159200	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr3:195148200-195159200	Weak transcription	Ovary	ovary
16	chr3:195148600-195161000	Weak transcription	K562	blood
17	chr3:195148600-195161800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:195150600-195161000	Weak transcription	NHLF	lung
19	chr3:195153400-195160600	Weak transcription	Primary T cells from cord blood	blood
20	chr3:195153600-195161000	Weak transcription	Fetal Lung	lung
21	chr3:195153800-195159200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:195153800-195159400	Weak transcription	Primary B cells from cord blood	blood
23	chr3:195154000-195160000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:195154000-195161000	Weak transcription	Fetal Intestine Small	intestine
25	chr3:195155200-195161200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:195155200-195161200	Weak transcription	Thymus	Thymus
27	chr3:195155200-195162000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:195155200-195162000	Weak transcription	Fetal Stomach	stomach
29	chr3:195155400-195159400	Weak transcription	Lung	lung
30	chr3:195156600-195159800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:195157000-195159800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:195157200-195159200	Weak transcription	GM12878-XiMat	blood
33	chr3:195157400-195162000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr3:195157600-195160000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:195157600-195160800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:195157600-195162000	Enhancers	Primary T cells fromperipheralblood	blood
37	chr3:195158000-195159600	Weak transcription	Psoas Muscle	Psoas
38	chr3:195158000-195161000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:195158200-195160000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:195158200-195160600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:195158400-195159400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:195158400-195159600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:195158400-195160600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:195158400-195161000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:195158800-195159400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:195159000-195159400	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr3:195159000-195159600	Enhancers	HMEC	breast
48	chr3:195159000-195159800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr3:195159000-195159800	Enhancers	NHEK	skin
50	chr3:195159000-195161000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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