Variant report

Variant	rs565660
Chromosome Location	chr10:6538303-6538304
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:6536042..6540361-chr10:6554431..6558363,4	K562	blood:
2	chr10:6515689..6518540-chr10:6536895..6539799,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs472317	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs527611	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs620736	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs622998	0.90[ASN][1000 genomes]
rs634492	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs648778	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs650652	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs790816	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv1047309	chr10:6495583-6714060	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv5687	chr10:6537209-6556751	Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6496600-6539200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr10:6499200-6562000	Weak transcription	Brain Anterior Caudate	brain
3	chr10:6501800-6557000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr10:6509200-6541200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr10:6510000-6572000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr10:6514000-6540000	Weak transcription	Psoas Muscle	Psoas
7	chr10:6517200-6557800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:6517600-6539600	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr10:6517600-6541800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr10:6518200-6556800	Weak transcription	Fetal Intestine Large	intestine
11	chr10:6519200-6544400	Weak transcription	Spleen	Spleen
12	chr10:6525800-6539400	Weak transcription	Primary B cells from cord blood	blood
13	chr10:6526600-6553000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr10:6527400-6542000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr10:6528400-6540800	Weak transcription	Brain Angular Gyrus	brain
16	chr10:6529000-6546200	Weak transcription	Esophagus	oesophagus
17	chr10:6529000-6552800	Weak transcription	Lung	lung
18	chr10:6530400-6552600	Weak transcription	K562	blood
19	chr10:6533600-6539800	Weak transcription	Brain Substantia Nigra	brain
20	chr10:6533800-6552800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr10:6534400-6545800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr10:6535400-6553400	Weak transcription	Gastric	stomach
23	chr10:6536000-6541400	Strong transcription	Fetal Muscle Leg	muscle
24	chr10:6536200-6539600	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr10:6536200-6540800	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr10:6536400-6540000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr10:6536600-6552800	Weak transcription	Fetal Intestine Small	intestine
28	chr10:6536800-6540800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr10:6537000-6540200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr10:6537000-6540400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:6537200-6540400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:6537200-6540800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr10:6537400-6552800	Weak transcription	Fetal Stomach	stomach
34	chr10:6537600-6539000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr10:6537600-6544200	Weak transcription	Pancreas	Pancrea
36	chr10:6537600-6552600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr10:6537800-6538400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr10:6537800-6538600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr10:6537800-6538800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr10:6537800-6540000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr10:6537800-6540200	Strong transcription	Primary T cells from cord blood	blood
42	chr10:6537800-6540200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr10:6537800-6540400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr10:6537800-6540400	Weak transcription	HMEC	breast
45	chr10:6537800-6540600	Strong transcription	Thymus	Thymus
46	chr10:6537800-6540600	Weak transcription	NHEK	skin
47	chr10:6537800-6543800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr10:6537800-6548600	Weak transcription	Brain Hippocampus Middle	brain
49	chr10:6537800-6548800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr10:6538000-6538600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links