Variant report

Variant	rs11644
Chromosome Location	chr2:113289032-113289033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113287458..113289198-chr2:113298107..113300239,2	MCF-7	breast:
2	chr2:113284316..113286214-chr2:113288766..113291061,2	K562	blood:
3	chr2:113284781..113289468-chr2:113295871..113300752,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POLR1B-2	chr2:113286258-113289988	NONHSAT073697

Variant related genes	Relation type
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10153558	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs10153801	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs11123137	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1127264	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899598	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs12465241	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465446	0.96[ASN][1000 genomes]
rs13030618	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs1437675	0.82[CHB][hapmap]
rs17043158	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs17043167	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs28542310	0.96[ASN][1000 genomes]
rs34082454	0.99[ASN][1000 genomes]
rs35419160	0.96[ASN][1000 genomes]
rs3849314	0.96[ASN][1000 genomes]
rs3910512	0.96[ASN][1000 genomes]
rs3980067	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4443006	0.85[EUR][1000 genomes]
rs56010201	0.95[ASN][1000 genomes]
rs62157527	0.87[ASN][1000 genomes]
rs62158577	0.88[EUR][1000 genomes]
rs6542059	0.92[ASN][1000 genomes]
rs6542060	0.92[ASN][1000 genomes]
rs6542061	0.96[ASN][1000 genomes]
rs6717635	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6718241	0.96[ASN][1000 genomes]
rs6718489	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760014	0.96[ASN][1000 genomes]
rs7569407	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7580213	0.96[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	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113241600-113292400	Weak transcription	Small Intestine	intestine
2	chr2:113260800-113298800	Weak transcription	Fetal Heart	heart
3	chr2:113267400-113290000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:113270600-113298800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:113277800-113290000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:113279000-113299200	Weak transcription	Psoas Muscle	Psoas
7	chr2:113281200-113299000	Weak transcription	Colonic Mucosa	Colon
8	chr2:113284800-113291200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:113285600-113291400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:113285800-113289800	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr2:113285800-113289800	Strong transcription	Ovary	ovary
12	chr2:113285800-113289800	Strong transcription	NHDF-Ad	bronchial
13	chr2:113285800-113290400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:113285800-113290600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr2:113285800-113290800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:113285800-113291200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:113285800-113291200	Strong transcription	Fetal Muscle Leg	muscle
18	chr2:113285800-113291200	Strong transcription	Thymus	Thymus
19	chr2:113285800-113291200	Strong transcription	Osteobl	bone
20	chr2:113285800-113291400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:113285800-113291400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:113285800-113291400	Strong transcription	Dnd41	blood
23	chr2:113285800-113291600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:113285800-113291600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:113286000-113289600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr2:113286000-113290000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:113286000-113291000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:113286000-113291200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:113286000-113291400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:113286000-113291400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:113286000-113291400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:113286000-113291400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr2:113286000-113291400	Strong transcription	Fetal Thymus	thymus
34	chr2:113286000-113291400	Strong transcription	Left Ventricle	heart
35	chr2:113286000-113291600	Strong transcription	Fetal Stomach	stomach
36	chr2:113286000-113291600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr2:113286000-113292200	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:113286000-113292200	Strong transcription	Fetal Brain Female	brain
39	chr2:113286200-113289400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr2:113286200-113289400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:113286200-113289600	Strong transcription	Brain Germinal Matrix	brain
42	chr2:113286200-113289800	Strong transcription	Aorta	Aorta
43	chr2:113286200-113290000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:113286200-113290000	Strong transcription	Primary B cells from cord blood	blood
45	chr2:113286200-113290000	Strong transcription	NH-A	brain
46	chr2:113286200-113290200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:113286200-113290200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:113286200-113290200	Strong transcription	Primary T cells from cord blood	blood
49	chr2:113286200-113290600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:113286200-113290600	Strong transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links