Variant report

Variant	rs16895001
Chromosome Location	chr6:163889780-163889781
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163889319..163891540-chr6:163964872..163967579,2	K562	blood:
2	chr6:163888891..163890676-chr6:164024271..164026675,2	K562	blood:
3	chr6:163833418..163836921-chr6:163889565..163892236,3	K562	blood:
4	chr6:163887956..163890806-chr6:163903233..163905754,2	K562	blood:
5	chr6:163882705..163885341-chr6:163888682..163891213,3	K562	blood:

Variant related genes	Relation type
ENSG00000270419	Chromatin interaction
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10484571	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10484572	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs10484573	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11962850	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11964510	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11964587	0.96[AFR][1000 genomes]
rs11964910	1.00[AMR][1000 genomes]
rs11965425	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11965709	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11966710	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11966885	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11966919	1.00[AMR][1000 genomes]
rs11966922	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11966958	0.91[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11969530	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11970766	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16888835	0.85[AFR][1000 genomes]
rs16888837	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs16895012	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16895056	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16895066	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16895078	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16895118	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs16895125	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16895139	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs3846780	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3903714	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56702350	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57292071	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57394768	1.00[AMR][1000 genomes]
rs57952819	1.00[AMR][1000 genomes]
rs59845233	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60965967	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61306342	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62428365	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6937286	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73784410	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73784416	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73787639	0.96[AFR][1000 genomes]
rs73787643	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73787648	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73787650	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7754815	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7755028	0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1797109	chr6:163834147-163908115	Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1019551	chr6:163842358-163965216	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1017495	chr6:163856399-163981095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv523664	chr6:163858237-163907885	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163878800-163910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:163879200-163891000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:163879200-163891200	Weak transcription	Fetal Kidney	kidney
4	chr6:163879400-163891000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:163880600-163890800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:163880600-163891000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:163880600-163891000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:163880600-163896600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:163880600-163897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:163880600-163903200	Weak transcription	Pancreas	Pancrea
11	chr6:163880600-163906600	Weak transcription	Gastric	stomach
12	chr6:163881600-163890400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:163881800-163890200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:163881800-163890600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:163881800-163890600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:163881800-163897600	Weak transcription	Ovary	ovary
17	chr6:163881800-163901000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:163881800-163910800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:163882000-163890600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:163882000-163891000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:163882000-163899800	Weak transcription	Placenta	Placenta
22	chr6:163882000-163900000	Weak transcription	Fetal Thymus	thymus
23	chr6:163882000-163906600	Weak transcription	Thymus	Thymus
24	chr6:163882200-163890600	Weak transcription	A549	lung
25	chr6:163882200-163890600	Weak transcription	Osteobl	bone
26	chr6:163882800-163890400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:163882800-163890800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:163883000-163891000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:163883000-163891000	Weak transcription	HUVEC	blood vessel
30	chr6:163883000-163895800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:163883000-163900800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr6:163883000-163900800	Weak transcription	NH-A	brain
33	chr6:163883000-163906800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:163883400-163890000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:163883400-163890200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:163883400-163890600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr6:163883800-163897000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:163884000-163890000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:163884000-163895800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:163884200-163891000	Enhancers	Brain Angular Gyrus	brain
41	chr6:163884400-163890000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
42	chr6:163884600-163890800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr6:163884600-163891200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:163884800-163890000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:163885200-163890200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr6:163885200-163893000	Weak transcription	Right Ventricle	heart
47	chr6:163885400-163890600	Weak transcription	HepG2	liver
48	chr6:163885600-163890200	Enhancers	Brain Substantia Nigra	brain
49	chr6:163886400-163889800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr6:163886600-163890800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links