Variant report

Variant	rs11969530
Chromosome Location	chr6:163902902-163902903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163896082..163898816-chr6:163902076..163903998,2	K562	blood:

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];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10484572	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs10484573	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11962850	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11964510	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11964587	0.85[AFR][1000 genomes]
rs11964910	1.00[AMR][1000 genomes]
rs11965425	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs11965709	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11966710	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11966885	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11966919	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11966922	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11966958	0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11970766	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16888835	0.81[AFR][1000 genomes]
rs16888837	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs16895001	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16895012	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16895056	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16895066	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16895078	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16895118	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs16895125	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16895139	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs3846780	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3903714	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56702350	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57292071	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57394768	1.00[AMR][1000 genomes]
rs57952819	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59845233	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60965967	1.00[AMR][1000 genomes]
rs61306342	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62428365	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6937286	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73784410	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73784416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73787639	0.85[AFR][1000 genomes]
rs73787643	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73787648	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73787650	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7754815	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7755028	0.92[YRI][hapmap];0.96[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:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163878800-163910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:163880600-163903200	Weak transcription	Pancreas	Pancrea
3	chr6:163880600-163906600	Weak transcription	Gastric	stomach
4	chr6:163881800-163910800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:163882000-163906600	Weak transcription	Thymus	Thymus
6	chr6:163883000-163906800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:163888400-163908200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:163890000-163906200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:163890800-163911400	Weak transcription	Osteobl	bone
10	chr6:163891400-163906400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:163891400-163910200	Weak transcription	HUVEC	blood vessel
12	chr6:163891600-163905000	Weak transcription	K562	blood
13	chr6:163892000-163904200	Weak transcription	NHDF-Ad	bronchial
14	chr6:163892200-163911400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:163892400-163903400	Weak transcription	Primary B cells from cord blood	blood
16	chr6:163892600-163906600	Weak transcription	NHEK	skin
17	chr6:163892600-163910400	Weak transcription	HMEC	breast
18	chr6:163893000-163912800	Weak transcription	Fetal Brain Male	brain
19	chr6:163893400-163912000	Weak transcription	Fetal Lung	lung
20	chr6:163893600-163904600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:163893600-163906200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:163893600-163906200	Weak transcription	A549	lung
23	chr6:163893600-163910200	Weak transcription	HSMMtube	muscle
24	chr6:163894400-163904800	Weak transcription	Esophagus	oesophagus
25	chr6:163896000-163906400	Weak transcription	Aorta	Aorta
26	chr6:163896600-163910800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr6:163897600-163905800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:163898000-163903200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:163898000-163907800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:163898200-163904000	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:163898200-163906600	Weak transcription	Spleen	Spleen
32	chr6:163898400-163903000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:163898400-163906400	Weak transcription	Ovary	ovary
34	chr6:163898400-163908200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:163898400-163909000	Weak transcription	Fetal Brain Female	brain
36	chr6:163898400-163911600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:163898400-163926000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:163898600-163907800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr6:163898800-163907200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:163898800-163908000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr6:163899000-163903600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr6:163899200-163904800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr6:163899200-163910200	Weak transcription	Hela-S3	cervix
44	chr6:163899400-163903000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:163899400-163905200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:163899600-163905000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:163899600-163910400	Weak transcription	NHLF	lung
48	chr6:163899800-163903000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:163899800-163903000	Strong transcription	HSMM	muscle
50	chr6:163899800-163903400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links