Variant report

Variant	rs11588634
Chromosome Location	chr1:151780686-151780687
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151763491..151766160-chr1:151779828..151782203,2	MCF-7	breast:
2	chr1:151777741..151780007-chr1:151780011..151781541,2	MCF-7	breast:
3	chr1:151752426..151754254-chr1:151778758..151780979,2	K562	blood:
4	chr1:151779245..151781251-chr1:151789971..151792071,2	K562	blood:
5	chr1:151774351..151777755-chr1:151779800..151782368,3	K562	blood:
6	chr1:151761843..151763864-chr1:151779499..151782273,2	MCF-7	breast:
7	chr1:151779508..151782077-chr1:151785257..151787936,2	K562	blood:
8	chr1:151779253..151781376-chr1:151783822..151786859,3	MCF-7	breast:
9	chr1:151779832..151781359-chr1:151797431..151800112,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000182134	Chromatin interaction
ENSG00000213171	Chromatin interaction
ENSG00000143365	Chromatin interaction
ENSG00000203288	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1054479	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10788809	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204884	0.87[ASN][1000 genomes]
rs11204892	0.80[EUR][1000 genomes]
rs11576810	1.00[CHB][hapmap]
rs11585294	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11586446	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs11586946	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11588258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810571	0.82[EUR][1000 genomes]
rs1196467	1.00[CHB][hapmap]
rs12238987	0.82[EUR][1000 genomes]
rs13376155	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1521185	0.82[EUR][1000 genomes]
rs17568246	1.00[CHB][hapmap]
rs3790514	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3811414	0.82[EUR][1000 genomes]
rs3811415	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3811416	0.82[EUR][1000 genomes]
rs4504897	0.82[EUR][1000 genomes]
rs4618976	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845356	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845570	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845579	0.82[EUR][1000 genomes]
rs6659705	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6664467	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6673002	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6673917	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6681093	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6683364	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6694952	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7007	1.00[CHB][hapmap]
rs7416415	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7542898	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010398	chr1:151761649-151790940	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv516369	chr1:151780177-151820324	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151764200-151787000	Weak transcription	Right Ventricle	heart
2	chr1:151764200-151792800	Weak transcription	Lung	lung
3	chr1:151764600-151782000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:151764600-151787600	Weak transcription	Primary T cells from cord blood	blood
5	chr1:151765400-151784200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:151770800-151787200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:151773200-151784800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:151773400-151784800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:151773400-151785000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:151774600-151787000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:151775800-151783600	Weak transcription	Psoas Muscle	Psoas
12	chr1:151776600-151787200	Weak transcription	Spleen	Spleen
13	chr1:151778000-151781800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:151778400-151786000	Strong transcription	Thymus	Thymus
15	chr1:151778400-151792800	Weak transcription	Left Ventricle	heart
16	chr1:151778600-151792000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:151778600-151802400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:151778800-151782600	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:151778800-151789200	Weak transcription	Fetal Intestine Small	intestine
20	chr1:151779000-151781600	Strong transcription	Pancreas	Pancrea
21	chr1:151779000-151787000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:151779200-151783800	Strong transcription	Liver	Liver
23	chr1:151779400-151780800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:151779400-151781200	Enhancers	Brain Substantia Nigra	brain
25	chr1:151779400-151783000	Enhancers	Brain Cingulate Gyrus	brain
26	chr1:151779400-151784200	Enhancers	Brain Hippocampus Middle	brain
27	chr1:151779600-151780800	Enhancers	Brain Germinal Matrix	brain
28	chr1:151779600-151781200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr1:151779800-151780800	Enhancers	Brain Angular Gyrus	brain
30	chr1:151779800-151780800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:151779800-151781800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:151780000-151780800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:151780000-151793400	Weak transcription	Stomach Mucosa	stomach
34	chr1:151780200-151780800	Strong transcription	Dnd41	blood
35	chr1:151780200-151781200	Enhancers	Brain Anterior Caudate	brain
36	chr1:151780200-151785400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr1:151780200-151786800	Weak transcription	Gastric	stomach
38	chr1:151780400-151780800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:151780400-151780800	Strong transcription	Fetal Thymus	thymus
40	chr1:151780600-151780800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:151780600-151780800	Enhancers	Adipose Nuclei	Adipose
42	chr1:151780600-151783600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links