Variant report

Variant	rs12592402
Chromosome Location	chr15:62349020-62349021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr15:62348987-62349145	HepG2	liver:	n/a	chr15:62349100-62349111

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62346359..62349999-chr15:62351464..62353902,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259251	TF binding region
ENSG00000129003	Chromatin interaction
ENSG00000259251	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10047986	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1030859	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1030860	0.87[ASN][1000 genomes]
rs1030861	0.87[ASN][1000 genomes]
rs10468026	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10519157	0.85[EUR][1000 genomes]
rs10851707	0.87[ASN][1000 genomes]
rs11071642	0.85[CEU][hapmap]
rs11071649	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11629596	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11632441	0.82[ASN][1000 genomes]
rs11633500	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11635977	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11635980	0.86[EUR][1000 genomes]
rs11638793	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11639482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12438690	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12438803	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12439356	0.96[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12440524	0.86[EUR][1000 genomes]
rs12442212	0.96[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12442448	0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12442675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12591155	0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs12591593	0.80[AFR][1000 genomes]
rs12593844	0.81[CEU][hapmap]
rs12594658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12594946	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12899801	0.81[CEU][hapmap]
rs12900645	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12900703	0.87[ASN][1000 genomes]
rs12912208	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs12913951	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1344601	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1436958	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1436959	0.81[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1436961	0.87[ASN][1000 genomes]
rs1436963	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1436964	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1436966	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs1534542	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs17205407	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17205463	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17271340	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs17271403	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17271431	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17271438	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1836996	0.85[ASN][1000 genomes]
rs2162062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2414753	0.86[CEU][hapmap]
rs2414754	0.82[CEU][hapmap]
rs28542204	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28837073	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2899677	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34096515	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34138933	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35123892	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3784445	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs3784633	0.96[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3784634	0.85[CEU][hapmap]
rs4143841	0.82[ASN][1000 genomes]
rs4143842	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4143843	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4564516	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774427	0.85[CEU][hapmap]
rs4775455	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775457	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4775458	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62007368	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62008532	0.86[EUR][1000 genomes]
rs7162536	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7172967	0.84[CEU][hapmap]
rs7177276	0.96[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7177711	0.96[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7178424	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7178540	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7178945	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs731820	0.96[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8025877	0.96[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8026008	0.96[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8027751	0.81[CEU][hapmap]
rs8029942	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs8032433	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8034216	0.89[CEU][hapmap]
rs8034335	0.89[CEU][hapmap]
rs8038932	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8039105	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs8039651	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs893156	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs893157	0.81[CEU][hapmap]
rs893158	0.96[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs933807	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9920758	0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs9989353	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904288	chr15:62146598-62356386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv904290	chr15:62175134-62356386	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv904294	chr15:62178695-62356386	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62244600-62350400	Weak transcription	Small Intestine	intestine
2	chr15:62300400-62351400	Weak transcription	Fetal Muscle Leg	muscle
3	chr15:62300600-62351800	Weak transcription	Lung	lung
4	chr15:62300800-62351600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr15:62302200-62351600	Weak transcription	Fetal Thymus	thymus
6	chr15:62302200-62351600	Weak transcription	Ovary	ovary
7	chr15:62321200-62350800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:62328000-62350000	Weak transcription	Brain Angular Gyrus	brain
9	chr15:62328200-62350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:62328400-62350800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:62328400-62351200	Weak transcription	NHLF	lung
12	chr15:62328400-62351400	Weak transcription	Osteobl	bone
13	chr15:62328800-62350000	Weak transcription	HUVEC	blood vessel
14	chr15:62328800-62350800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:62329000-62350400	Weak transcription	NHDF-Ad	bronchial
16	chr15:62333400-62351400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:62333600-62351400	Weak transcription	HSMM	muscle
18	chr15:62333800-62350600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:62336000-62350400	Weak transcription	Fetal Intestine Large	intestine
20	chr15:62339600-62350800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:62342200-62351400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr15:62343000-62350600	Weak transcription	K562	blood
23	chr15:62344000-62350400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr15:62344000-62350800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:62344000-62350800	Weak transcription	Left Ventricle	heart
26	chr15:62344000-62350800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:62344000-62351200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr15:62345600-62349800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr15:62345600-62349800	Weak transcription	Colon Smooth Muscle	Colon
30	chr15:62345600-62351400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:62345800-62351000	Weak transcription	Fetal Lung	lung
32	chr15:62346000-62350000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr15:62346000-62350000	Weak transcription	Hela-S3	cervix
34	chr15:62346000-62350800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:62346000-62351000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:62346200-62349600	Weak transcription	Primary T cells from cord blood	blood
37	chr15:62346200-62349600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr15:62346200-62350000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:62346200-62350400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:62346200-62350400	Weak transcription	Adipose Nuclei	Adipose
41	chr15:62346200-62350400	Weak transcription	Stomach Mucosa	stomach
42	chr15:62346200-62350600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:62346200-62350600	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:62346200-62350800	Weak transcription	Right Ventricle	heart
45	chr15:62346200-62350800	Weak transcription	Spleen	Spleen
46	chr15:62346200-62351000	Weak transcription	Psoas Muscle	Psoas
47	chr15:62346200-62351000	Weak transcription	Right Atrium	heart
48	chr15:62346200-62351400	Weak transcription	Brain Substantia Nigra	brain
49	chr15:62346200-62351400	Weak transcription	Thymus	Thymus
50	chr15:62346400-62350400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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