Variant report

Variant	rs9405833
Chromosome Location	chr6:5441653-5441654
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	chr6:5431881..5436604-chr6:5436753..5441713,4	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10900967	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12198170	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364557	0.82[CEU][hapmap]
rs1895645	0.89[CEU][hapmap]
rs200198	0.83[CHB][hapmap]
rs200201	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs2032988	0.85[EUR][1000 genomes]
rs2113691	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326609	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2326610	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2503813	0.85[CEU][hapmap]
rs6922067	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9328299	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9328300	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9328301	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9328302	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9378949	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9378950	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9392684	0.82[CEU][hapmap]
rs9392686	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405268	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405832	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv830578	chr6:5264086-5455570	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv883418	chr6:5307432-5501389	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1015643	chr6:5311590-5452427	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1030744	chr6:5328012-5458222	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1023027	chr6:5377308-5556749	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv538121	chr6:5377308-5556749	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1022505	chr6:5388025-5449240	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv600885	chr6:5424762-5455161	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv600886	chr6:5426265-5511614	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5403400-5445200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:5413400-5442800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:5421600-5455000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:5421600-5455400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:5421600-5457400	Weak transcription	Fetal Intestine Small	intestine
6	chr6:5422800-5444000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr6:5429200-5443000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:5429800-5442600	Weak transcription	NHEK	skin
9	chr6:5430000-5443600	Weak transcription	Right Ventricle	heart
10	chr6:5430400-5441800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:5430400-5443600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:5430600-5443600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:5433200-5443400	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:5433400-5443600	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:5433400-5453800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:5433600-5457400	Weak transcription	Left Ventricle	heart
17	chr6:5433600-5461400	Weak transcription	Fetal Stomach	stomach
18	chr6:5433800-5443800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:5434200-5487000	Weak transcription	Aorta	Aorta
20	chr6:5435600-5443600	Weak transcription	Esophagus	oesophagus
21	chr6:5436400-5446600	Weak transcription	HSMM	muscle
22	chr6:5436400-5447200	Weak transcription	HSMMtube	muscle
23	chr6:5436600-5443800	Weak transcription	Primary B cells from cord blood	blood
24	chr6:5437400-5471200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:5438200-5443600	Weak transcription	Psoas Muscle	Psoas
26	chr6:5438200-5443600	Weak transcription	Right Atrium	heart
27	chr6:5438200-5445800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr6:5438200-5471200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:5439600-5443800	Weak transcription	Lung	lung
30	chr6:5439600-5459800	Weak transcription	Primary T cells from cord blood	blood
31	chr6:5440200-5442800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:5440200-5442800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr6:5440200-5442800	Weak transcription	Osteobl	bone
34	chr6:5440200-5443200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:5440200-5443600	Weak transcription	Gastric	stomach
36	chr6:5440200-5443600	Weak transcription	Pancreas	Pancrea
37	chr6:5440200-5443800	Weak transcription	Fetal Thymus	thymus
38	chr6:5440400-5454800	Weak transcription	Liver	Liver
39	chr6:5441000-5444800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links