Variant report

Variant	rs533201
Chromosome Location	chr6:147606395-147606396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:147223283..147224171-chr6:147605957..147606781,4	MCF-7	breast:
2	chr6:147534848..147537270-chr6:147604730..147607356,2	K562	blood:
3	chr6:147522804..147525350-chr6:147604658..147607399,2	MCF-7	breast:
4	chr6:147178646..147179531-chr6:147606189..147606807,2	MCF-7	breast:
5	chr6:147178650..147179155-chr6:147605934..147606927,2	K562	blood:
6	chr6:147178362..147178887-chr6:147606280..147606878,2	MCF-7	breast:
7	chr6:147605533..147608299-chr6:147613299..147616141,2	K562	blood:

Variant related genes	Relation type
ENSG00000233452	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1039083	0.99[EUR][1000 genomes]
rs1039084	0.82[EUR][1000 genomes]
rs1039085	0.99[EUR][1000 genomes]
rs1039086	0.81[EUR][1000 genomes]
rs1147844	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1147845	0.96[EUR][1000 genomes]
rs1147846	0.81[EUR][1000 genomes]
rs1147847	0.82[EUR][1000 genomes]
rs12527235	0.81[EUR][1000 genomes]
rs1496031	1.00[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap]
rs1496033	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1496034	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1660687	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1765028	0.87[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs1992389	0.82[EUR][1000 genomes]
rs2047286	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2068111	0.99[EUR][1000 genomes]
rs2119490	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2218221	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2502732	0.81[EUR][1000 genomes]
rs2582925	0.98[EUR][1000 genomes]
rs2582929	0.82[EUR][1000 genomes]
rs2786180	0.84[GIH][hapmap]
rs2786183	0.82[EUR][1000 genomes]
rs2786184	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2786185	0.83[EUR][1000 genomes]
rs2850177	0.98[EUR][1000 genomes]
rs2850178	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs474990	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs486867	0.98[EUR][1000 genomes]
rs4896904	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4896905	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4896906	0.89[EUR][1000 genomes]
rs4896908	0.86[EUR][1000 genomes]
rs519630	0.90[ASN][1000 genomes]
rs562417	0.81[EUR][1000 genomes]
rs577877	0.95[EUR][1000 genomes]
rs584456	0.82[EUR][1000 genomes]
rs588273	0.96[EUR][1000 genomes]
rs591355	0.81[EUR][1000 genomes]
rs597631	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs598038	0.99[EUR][1000 genomes]
rs608147	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs614476	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs617975	0.98[EUR][1000 genomes]
rs618474	0.81[EUR][1000 genomes]
rs619175	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs619626	0.81[EUR][1000 genomes]
rs620715	0.80[EUR][1000 genomes]
rs62435630	0.82[EUR][1000 genomes]
rs633603	0.81[EUR][1000 genomes]
rs659399	0.82[EUR][1000 genomes]
rs664203	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6928919	0.82[EUR][1000 genomes]
rs6932613	0.81[EUR][1000 genomes]
rs7748995	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7762087	0.82[EUR][1000 genomes]
rs9373523	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9377048	0.82[EUR][1000 genomes]
rs9390458	0.84[CEU][hapmap];0.80[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9390462	0.81[AMR][1000 genomes]
rs9399598	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs9403852	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9497759	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs995697	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019245	chr6:147350834-147609776	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538467	chr6:147350834-147609776	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886752	chr6:147443480-147729477	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv886753	chr6:147526508-147680291	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv470864	chr6:147539165-147709179	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv886754	chr6:147539165-147729477	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv604840	chr6:147539165-147730324	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	esv1832155	chr6:147554900-147715464	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv886755	chr6:147577646-147729477	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv886756	chr6:147580697-147729477	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv830839	chr6:147584914-147757264	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv522406	chr6:147591022-147635413	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv886757	chr6:147591022-147729477	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147545600-147617000	Weak transcription	Small Intestine	intestine
2	chr6:147549400-147616800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr6:147564400-147619000	Weak transcription	Hela-S3	cervix
4	chr6:147564600-147608800	Weak transcription	NH-A	brain
5	chr6:147564600-147617000	Weak transcription	Fetal Kidney	kidney
6	chr6:147570600-147609000	Weak transcription	Brain Substantia Nigra	brain
7	chr6:147572600-147609600	Weak transcription	Thymus	Thymus
8	chr6:147572600-147610200	Weak transcription	Esophagus	oesophagus
9	chr6:147572800-147617000	Weak transcription	Right Ventricle	heart
10	chr6:147573000-147616600	Weak transcription	Ovary	ovary
11	chr6:147573000-147616800	Weak transcription	Aorta	Aorta
12	chr6:147573200-147610000	Weak transcription	Fetal Stomach	stomach
13	chr6:147573200-147617000	Weak transcription	Spleen	Spleen
14	chr6:147573400-147609200	Weak transcription	Pancreas	Pancrea
15	chr6:147573800-147608600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:147574400-147616600	Weak transcription	Fetal Brain Female	brain
17	chr6:147576800-147609800	Weak transcription	HSMMtube	muscle
18	chr6:147578200-147616800	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:147579200-147610000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:147579400-147609800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:147584400-147684600	Weak transcription	Brain Angular Gyrus	brain
22	chr6:147585800-147617200	Weak transcription	Fetal Brain Male	brain
23	chr6:147587000-147618000	Weak transcription	Psoas Muscle	Psoas
24	chr6:147587600-147609400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:147588600-147616800	Weak transcription	Brain Germinal Matrix	brain
26	chr6:147588800-147617000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:147589400-147608600	Weak transcription	NHEK	skin
28	chr6:147590400-147616400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:147593200-147608600	Weak transcription	A549	lung
30	chr6:147595000-147610000	Weak transcription	Lung	lung
31	chr6:147595800-147616600	Weak transcription	Colonic Mucosa	Colon
32	chr6:147598000-147617000	Strong transcription	K562	blood
33	chr6:147598200-147616600	Weak transcription	Gastric	stomach
34	chr6:147599400-147617000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:147599600-147617000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:147600200-147608600	Weak transcription	HUVEC	blood vessel
37	chr6:147600200-147608800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr6:147600200-147609000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:147600200-147609200	Weak transcription	Left Ventricle	heart
40	chr6:147600200-147615000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:147600200-147616400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:147600200-147616400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr6:147600200-147616600	Weak transcription	Adipose Nuclei	Adipose
44	chr6:147600200-147616600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:147600200-147616800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:147600200-147618800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:147600400-147616600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:147600800-147616200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr6:147600800-147617000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr6:147601000-147608800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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