Variant report

Variant	rs440613
Chromosome Location	chr6:149778892-149778893
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	GATA2	chr6:149778693-149779134	SH-SY5Y	brain:	n/a	n/a
2	MYC	chr6:149778825-149778946	K562	blood:	n/a	n/a
3	BCL3	chr6:149778683-149778929	GM12878	blood:	n/a	n/a
4	GATA3	chr6:149778673-149779081	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
ZC3H12D	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11155656	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11155657	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs112225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190660	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1737336	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1737337	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1749227	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1768341	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1999970	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2095849	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs237004	0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs237006	0.86[ASN][1000 genomes]
rs237007	0.86[ASN][1000 genomes]
rs237008	0.84[ASN][1000 genomes]
rs367133	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs367161	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367812	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs370471	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372994	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373596	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs374616	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs376269	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs376757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377454	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs377532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381226	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs381793	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382084	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382720	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs383092	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384163	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384306	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs384913	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385303	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385657	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs388335	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs391875	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs392928	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs392932	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs393713	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394526	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs395037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398159	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs403419	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405486	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs407260	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409196	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs411308	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414956	0.86[ASN][1000 genomes]
rs416044	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs416262	0.86[ASN][1000 genomes]
rs419562	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs419997	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421037	0.88[ASN][1000 genomes]
rs425278	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs430192	0.86[ASN][1000 genomes]
rs431362	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs431978	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs432582	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs436645	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs437931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs439369	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439495	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs450344	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499270	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543489	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611311	0.83[ASN][1000 genomes]
rs677525	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs786749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786750	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs786751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786757	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs814181	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9485396	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS 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	nsv470866	chr6:149744632-149806552	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5533	chr6:149748047-149793072	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv464076	chr6:149755695-149798835	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv604846	chr6:149755695-149798835	ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149768400-149779400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:149769600-149782800	Strong transcription	Primary B cells from peripheral blood	blood
3	chr6:149769600-149787200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:149769800-149779800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:149770000-149779600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:149770000-149785200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:149772000-149788800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:149772600-149779400	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:149772600-149787000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:149773000-149779600	Weak transcription	Primary T cells from cord blood	blood
11	chr6:149773000-149783400	Strong transcription	Primary B cells from cord blood	blood
12	chr6:149775600-149779600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:149775800-149780800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:149776000-149780600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:149776200-149780600	Weak transcription	NH-A	brain
16	chr6:149776200-149785200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:149776200-149789600	Weak transcription	Fetal Thymus	thymus
18	chr6:149776400-149779400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:149776400-149780600	Weak transcription	Osteobl	bone
20	chr6:149776400-149784400	Weak transcription	Small Intestine	intestine
21	chr6:149776400-149784800	Weak transcription	HepG2	liver
22	chr6:149776400-149785200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr6:149776400-149785400	Weak transcription	HSMMtube	muscle
24	chr6:149776600-149779400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr6:149776600-149780600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:149776600-149781600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr6:149776600-149785200	Weak transcription	Colonic Mucosa	Colon
28	chr6:149776800-149779600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:149776800-149780000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:149776800-149782600	Weak transcription	Stomach Mucosa	stomach
31	chr6:149776800-149785200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:149776800-149785200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:149776800-149785200	Weak transcription	Hela-S3	cervix
34	chr6:149776800-149785400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:149776800-149802000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:149777000-149779800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:149777000-149780800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr6:149777600-149779200	Enhancers	Fetal Heart	heart
39	chr6:149777600-149779800	Enhancers	Right Ventricle	heart
40	chr6:149778000-149779000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr6:149778000-149779000	Enhancers	Ovary	ovary
42	chr6:149778000-149781400	Strong transcription	GM12878-XiMat	blood
43	chr6:149778000-149783400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr6:149778200-149779200	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr6:149778200-149779600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:149778200-149779800	Enhancers	Fetal Lung	lung
47	chr6:149778200-149781600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr6:149778200-149783600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr6:149778400-149783000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:149778400-149785400	Weak transcription	Gastric	stomach

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