Variant report

Variant	rs10189379
Chromosome Location	chr2:55263143-55263144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55255745..55260236-chr2:55263069..55266549,5	K562	blood:
2	chr2:55261847..55264222-chr2:55276252..55278273,3	MCF-7	breast:
3	chr2:55251258..55253325-chr2:55261770..55263673,2	K562	blood:
4	chr2:55257553..55263983-chr2:55266645..55270936,7	K562	blood:
5	chr2:55256384..55258349-chr2:55263077..55265384,2	K562	blood:
6	chr2:55261058..55265438-chr2:55268460..55270489,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10170340	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10210840	0.85[YRI][hapmap]
rs10496036	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10496037	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs12464447	0.83[ASN][1000 genomes]
rs12464595	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12469804	0.90[CHB][hapmap]
rs12475787	0.85[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs12475904	0.86[ASN][1000 genomes]
rs12479297	0.94[ASN][1000 genomes]
rs1348528	1.00[CHB][hapmap]
rs17046570	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17046594	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17347089	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17418675	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1822618	1.00[CHB][hapmap]
rs2864049	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56013263	0.90[ASN][1000 genomes]
rs60825248	0.82[ASN][1000 genomes]
rs6545467	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545468	0.80[EUR][1000 genomes]
rs6713935	0.90[CHB][hapmap]
rs67156582	0.82[ASN][1000 genomes]
rs6730728	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72795440	0.93[ASN][1000 genomes]
rs7584354	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7584386	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7601625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs887	0.90[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
2	chr2:55241000-55272400	Weak transcription	Fetal Kidney	kidney
3	chr2:55245600-55265600	Weak transcription	Stomach Mucosa	stomach
4	chr2:55250400-55271000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:55250400-55274000	Weak transcription	Pancreas	Pancrea
6	chr2:55253400-55273000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:55254200-55269800	Weak transcription	Aorta	Aorta
8	chr2:55254200-55270400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:55254800-55265000	Enhancers	Brain Substantia Nigra	brain
10	chr2:55255400-55272600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:55255400-55272600	Weak transcription	Fetal Intestine Small	intestine
12	chr2:55256400-55266600	Weak transcription	Left Ventricle	heart
13	chr2:55256400-55270400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:55256600-55264000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:55256600-55265200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:55256800-55264200	Weak transcription	HSMMtube	muscle
17	chr2:55259000-55264400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:55259000-55264600	Weak transcription	HMEC	breast
19	chr2:55259000-55264600	Weak transcription	NHLF	lung
20	chr2:55259000-55265600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:55259000-55267400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:55259000-55272800	Weak transcription	Small Intestine	intestine
23	chr2:55259200-55264400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:55259200-55272800	Weak transcription	Fetal Heart	heart
25	chr2:55259400-55264400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:55259400-55275200	Weak transcription	Esophagus	oesophagus
27	chr2:55259600-55263400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:55259600-55263400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr2:55260000-55264000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:55260000-55264600	Weak transcription	Fetal Brain Male	brain
31	chr2:55260000-55265000	Strong transcription	HSMM	muscle
32	chr2:55260000-55265600	Weak transcription	NHEK	skin
33	chr2:55260600-55264400	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:55260800-55263200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:55260800-55263200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr2:55260800-55263400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:55260800-55264200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:55260800-55264400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:55260800-55264400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:55260800-55264600	Weak transcription	Gastric	stomach
41	chr2:55260800-55266000	Weak transcription	Adipose Nuclei	Adipose
42	chr2:55260800-55266200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:55260800-55266600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:55260800-55270400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:55260800-55271200	Weak transcription	Lung	lung
46	chr2:55260800-55271200	Weak transcription	Right Atrium	heart
47	chr2:55260800-55272000	Weak transcription	NH-A	brain
48	chr2:55260800-55272400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:55260800-55273200	Weak transcription	Psoas Muscle	Psoas
50	chr2:55261000-55263200	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links