Variant report

Variant	rs41270062
Chromosome Location	chr6:35218274-35218275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35215391..35219513-chr6:35220347..35223844,6	K562	blood:
2	chr6:35217807..35220229-chr6:35225285..35228255,2	MCF-7	breast:
3	chr6:35216569..35221401-chr6:35225274..35227948,4	MCF-7	breast:
4	chr6:35217337..35219867-chr6:35227257..35229632,2	K562	blood:

Variant related genes	Relation type
ENSG00000065029	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1034450	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10428744	1.00[ASN][1000 genomes]
rs11962521	1.00[ASN][1000 genomes]
rs11962524	1.00[ASN][1000 genomes]
rs12110520	1.00[ASN][1000 genomes]
rs12110664	1.00[ASN][1000 genomes]
rs12111424	1.00[ASN][1000 genomes]
rs16868695	1.00[ASN][1000 genomes]
rs16868699	1.00[ASN][1000 genomes]
rs16872293	1.00[ASN][1000 genomes]
rs16873902	1.00[AMR][1000 genomes]
rs16874216	1.00[ASN][1000 genomes]
rs17511800	1.00[AMR][1000 genomes]
rs2004	1.00[ASN][1000 genomes]
rs2187903	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228265	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28627111	1.00[ASN][1000 genomes]
rs2894400	1.00[ASN][1000 genomes]
rs34278260	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270046	1.00[ASN][1000 genomes]
rs45482297	1.00[ASN][1000 genomes]
rs56809926	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57229653	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57468283	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57794912	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57976333	1.00[ASN][1000 genomes]
rs58796597	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58850273	1.00[ASN][1000 genomes]
rs59757151	1.00[ASN][1000 genomes]
rs59895076	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60086237	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60113507	1.00[ASN][1000 genomes]
rs60569490	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61592141	1.00[ASN][1000 genomes]
rs61734578	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457817	1.00[ASN][1000 genomes]
rs6900879	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901580	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904477	1.00[ASN][1000 genomes]
rs6905732	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911817	1.00[ASN][1000 genomes]
rs6923025	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934083	1.00[ASN][1000 genomes]
rs6938138	1.00[ASN][1000 genomes]
rs6939017	1.00[ASN][1000 genomes]
rs73403830	1.00[ASN][1000 genomes]
rs73403834	1.00[ASN][1000 genomes]
rs73403837	1.00[ASN][1000 genomes]
rs73403843	1.00[ASN][1000 genomes]
rs73403847	1.00[ASN][1000 genomes]
rs73403887	1.00[ASN][1000 genomes]
rs73405709	1.00[ASN][1000 genomes]
rs73405725	1.00[ASN][1000 genomes]
rs73405759	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73405765	1.00[ASN][1000 genomes]
rs73405768	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73405774	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73405795	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73405799	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73407610	1.00[ASN][1000 genomes]
rs73407613	1.00[ASN][1000 genomes]
rs73407619	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407641	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407650	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407675	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409710	1.00[ASN][1000 genomes]
rs73409758	1.00[ASN][1000 genomes]
rs73409765	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409769	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409774	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409778	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409793	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73411706	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73411720	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73411726	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73411781	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73411797	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73746425	1.00[ASN][1000 genomes]
rs73746430	1.00[ASN][1000 genomes]
rs743965	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773319	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820102	1.00[ASN][1000 genomes]
rs9462062	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462064	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469960	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469967	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9658079	1.00[AMR][1000 genomes]
rs9658127	1.00[ASN][1000 genomes]
rs9658129	1.00[AMR][1000 genomes]
rs9658131	1.00[ASN][1000 genomes]
rs9658132	1.00[AMR][1000 genomes]
rs9658135	1.00[AMR][1000 genomes]
rs9658149	1.00[AMR][1000 genomes]
rs9658170	1.00[AMR][1000 genomes]
rs9942465	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3428128	chr6:35150524-35225843	Bivalent Enhancer Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35191400-35226000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:35194000-35225600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:35199600-35226600	Weak transcription	Esophagus	oesophagus
4	chr6:35199800-35226200	Weak transcription	Pancreas	Pancrea
5	chr6:35200600-35225000	Weak transcription	Fetal Brain Male	brain
6	chr6:35201400-35226200	Weak transcription	Stomach Mucosa	stomach
7	chr6:35202600-35225800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:35203400-35226000	Weak transcription	HSMMtube	muscle
9	chr6:35205600-35226000	Weak transcription	HSMM	muscle
10	chr6:35207400-35226200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:35207800-35224000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:35208200-35226000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:35208400-35226000	Weak transcription	NHEK	skin
14	chr6:35208600-35220200	Strong transcription	Fetal Stomach	stomach
15	chr6:35209800-35220000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:35209800-35226400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:35210400-35219000	Weak transcription	Placenta	Placenta
18	chr6:35210600-35225400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:35211000-35226000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:35212400-35226000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr6:35213200-35226200	Weak transcription	Gastric	stomach
22	chr6:35213400-35218800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr6:35213400-35225600	Weak transcription	Fetal Kidney	kidney
24	chr6:35213400-35226000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:35213400-35226000	Weak transcription	NH-A	brain
26	chr6:35213600-35225600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:35213800-35218600	Weak transcription	Spleen	Spleen
28	chr6:35213800-35219600	Weak transcription	Thymus	Thymus
29	chr6:35214000-35218600	Weak transcription	Lung	lung
30	chr6:35214000-35225000	Weak transcription	HepG2	liver
31	chr6:35214000-35225400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:35214000-35225800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr6:35214000-35226000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:35214200-35219400	Weak transcription	Primary T cells from cord blood	blood
35	chr6:35214400-35225000	Weak transcription	Brain Germinal Matrix	brain
36	chr6:35214400-35225400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:35214400-35225600	Weak transcription	Dnd41	blood
38	chr6:35214400-35225800	Weak transcription	Fetal Lung	lung
39	chr6:35214400-35226000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:35214400-35226600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:35214600-35225400	Weak transcription	Fetal Brain Female	brain
42	chr6:35214600-35226200	Weak transcription	Aorta	Aorta
43	chr6:35215000-35226000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:35216000-35218800	Enhancers	Brain Anterior Caudate	brain
45	chr6:35216000-35218800	Enhancers	Brain Hippocampus Middle	brain
46	chr6:35216200-35218800	Enhancers	Brain Substantia Nigra	brain
47	chr6:35216400-35219400	Enhancers	Right Ventricle	heart
48	chr6:35216400-35220000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:35216400-35225800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:35216600-35220600	Strong transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links