Variant report

Variant	rs728408
Chromosome Location	chr3:52517206-52517207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52516724-52517362	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:52516957-52517327	K562	blood:	n/a	n/a
3	POLR2A	chr3:52516574-52517751	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:52516865-52517267	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr3:52515974-52517907	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:52516116-52517961	GM12892	blood:	n/a	n/a
7	POLR2A	chr3:52516752-52517486	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:52516777-52517342	GM12891	blood:	n/a	n/a
9	POLR2A	chr3:52516498-52518048	GM12892	blood:	n/a	n/a
10	POLR2A	chr3:52516618-52517311	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:52516712-52517410	K562	blood:	n/a	n/a
12	POLR2A	chr3:52516738-52517894	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:52517178-52517278	HepG2	liver:	n/a	n/a
14	CTCF	chr3:52517180-52517330	BJ	skin:	n/a	n/a
15	POLR2A	chr3:52515256-52517667	K562	blood:	n/a	n/a
16	POLR2A	chr3:52516264-52517876	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:52516410-52517372	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:52515059-52518160	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:52517022-52517344	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:52517136-52517515	U87	brain:	n/a	n/a
21	POLR2A	chr3:52516830-52517330	HL-60	blood:	n/a	n/a
22	POLR2A	chr3:52516687-52517797	GM12891	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52514786..52517540-chr3:52524026..52525964,2	K562	blood:
2	chr3:52517051..52518693-chr3:52528843..52530538,2	K562	blood:

No data

Variant related genes	Relation type
NISCH	TF binding region
ENSG00000010327	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1011062	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1011063	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1011064	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1035002	0.91[EUR][1000 genomes]
rs1035003	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1077142	1.00[JPT][hapmap]
rs10865972	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11707864	1.00[JPT][hapmap]
rs11707931	1.00[JPT][hapmap]
rs11709658	1.00[JPT][hapmap]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[JPT][hapmap]
rs11716017	1.00[JPT][hapmap]
rs11718125	1.00[JPT][hapmap]
rs11721286	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123598	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs123602	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs123603	1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs13071708	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs13074649	0.93[EUR][1000 genomes]
rs13075370	1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13089892	1.00[ASW][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs13091360	1.00[JPT][hapmap]
rs13091545	1.00[JPT][hapmap]
rs1541495	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[JPT][hapmap]
rs2016575	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2109557	0.81[EUR][1000 genomes]
rs2109558	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159607	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2215466	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs2335640	1.00[JPT][hapmap]
rs2335928	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2335929	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2878549	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs34261027	1.00[ASN][1000 genomes]
rs34762015	1.00[JPT][hapmap]
rs35860312	1.00[JPT][hapmap]
rs3755810	1.00[ASW][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs3774409	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs3796343	1.00[JPT][hapmap]
rs390802	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs409803	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41292858	1.00[AFR][1000 genomes]
rs419050	1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs419604	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs419752	1.00[JPT][hapmap];0.86[TSI][hapmap]
rs4312651	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687541	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4687543	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687544	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687545	1.00[AFR][1000 genomes]
rs4687614	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs4687616	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4687617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687618	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687619	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687621	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs498778	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs498946	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs575476	0.81[EUR][1000 genomes]
rs613519	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs634382	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6414568	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6445386	1.00[JPT][hapmap]
rs6445483	0.81[EUR][1000 genomes]
rs6445484	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6445485	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6445486	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6445506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676034	1.00[ASW][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs6763882	1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6782162	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6784615	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787493	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6810027	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs758800	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs758802	1.00[AFR][1000 genomes]
rs758803	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7620015	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs82825	1.00[JPT][hapmap]
rs887514	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887515	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs929528	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs929529	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9846089	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9847332	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9850471	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9855470	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9863753	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9867823	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590304	chr3:52517206-52529266	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
2	chr3:52491800-52524000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:52491800-52527000	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:52492400-52517400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:52493000-52527800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:52498600-52527200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr3:52499400-52527800	Strong transcription	Primary T cells from cord blood	blood
10	chr3:52499600-52529200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:52501600-52528800	Strong transcription	Fetal Intestine Small	intestine
12	chr3:52504200-52526600	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr3:52504200-52526800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:52504200-52527400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:52504200-52527400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:52504200-52527600	Strong transcription	Dnd41	blood
17	chr3:52504200-52527800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:52504200-52528000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr3:52504200-52528000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:52504200-52528600	Strong transcription	Brain Germinal Matrix	brain
21	chr3:52504400-52517400	Strong transcription	NHEK	skin
22	chr3:52504400-52517600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:52504400-52523600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:52504400-52523800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr3:52504400-52527400	Strong transcription	Osteobl	bone
26	chr3:52504400-52527600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:52504400-52527600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:52504400-52528000	Strong transcription	Fetal Brain Female	brain
29	chr3:52504600-52517400	Strong transcription	Fetal Lung	lung
30	chr3:52504600-52518000	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:52504800-52518000	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:52504800-52518800	Strong transcription	Colonic Mucosa	Colon
33	chr3:52504800-52520000	Strong transcription	HSMM	muscle
34	chr3:52504800-52521400	Strong transcription	Fetal Intestine Large	intestine
35	chr3:52504800-52523000	Strong transcription	HUVEC	blood vessel
36	chr3:52504800-52523800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:52504800-52527400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:52504800-52528000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:52505000-52517400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:52505000-52517400	Strong transcription	Aorta	Aorta
41	chr3:52505000-52517400	Strong transcription	Rectal Smooth Muscle	rectum
42	chr3:52505000-52517400	Strong transcription	HepG2	liver
43	chr3:52505000-52527000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:52505600-52518000	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr3:52506200-52523600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:52506400-52527400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:52506600-52517400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:52506600-52517400	Strong transcription	Brain Hippocampus Middle	brain
49	chr3:52507400-52527800	Strong transcription	Fetal Thymus	thymus
50	chr3:52508000-52523000	Weak transcription	Stomach Mucosa	stomach

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