Variant report

Variant	rs12152700
Chromosome Location	chr4:27006651-27006652
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:27002739..27005621-chr4:27005771..27008805,3	K562	blood:

Variant related genes	Relation type
ENSG00000109689	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10010180	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10019691	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1012550	0.96[CEU][hapmap]
rs10433805	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10939147	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs16878653	0.95[CEU][hapmap]
rs16878671	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28570016	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28668622	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2871256	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2871258	0.88[ASN][1000 genomes]
rs35499018	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4692136	0.96[YRI][hapmap]
rs4692142	0.84[ASN][1000 genomes]
rs6448491	0.88[ASN][1000 genomes]
rs6830950	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6833149	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6838936	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855865	0.95[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6856381	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7669818	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7679403	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7680613	0.88[ASN][1000 genomes]
rs7681802	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7693687	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.86[ASN][1000 genomes]
rs7695335	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7700108	0.95[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9291487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9995206	0.92[AMR][1000 genomes]
rs9998971	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv461312	chr4:26844674-27078376	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv593872	chr4:26844674-27078376	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1000568	chr4:26886920-27049554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12152700	STIM2	cis	uninvolved skin	skin_eQTL
rs12152700	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs12152700	STIM2	cis	normal skin	skin_eQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26978400-27019200	Weak transcription	Fetal Intestine Small	intestine
2	chr4:26980400-27019400	Weak transcription	Left Ventricle	heart
3	chr4:26985400-27019400	Weak transcription	Esophagus	oesophagus
4	chr4:26989000-27010000	Weak transcription	Thymus	Thymus
5	chr4:26989000-27010400	Weak transcription	Fetal Thymus	thymus
6	chr4:26989400-27024800	Weak transcription	Psoas Muscle	Psoas
7	chr4:26989600-27027000	Weak transcription	HepG2	liver
8	chr4:26994800-27011000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:26995000-27019000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:26995000-27028200	Weak transcription	Pancreas	Pancrea
11	chr4:26995400-27009800	Weak transcription	Adipose Nuclei	Adipose
12	chr4:26996200-27015400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:26996400-27007600	Weak transcription	Brain Angular Gyrus	brain
14	chr4:26996400-27026200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:26996600-27007600	Weak transcription	Ovary	ovary
16	chr4:26996600-27011800	Weak transcription	Brain Anterior Caudate	brain
17	chr4:26996600-27018400	Weak transcription	Fetal Intestine Large	intestine
18	chr4:26996600-27019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:26996800-27007200	Weak transcription	Brain Substantia Nigra	brain
20	chr4:26996800-27019200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:26997000-27007600	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:26997400-27019200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:27001200-27029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:27001600-27006800	Weak transcription	Liver	Liver
25	chr4:27001600-27019000	Weak transcription	Spleen	Spleen
26	chr4:27002000-27019200	Weak transcription	Lung	lung
27	chr4:27002000-27019200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr4:27002200-27013000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:27002600-27011200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:27002800-27011800	Weak transcription	Stomach Mucosa	stomach
31	chr4:27002800-27026000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:27003400-27007800	Weak transcription	Aorta	Aorta
33	chr4:27003400-27011600	Strong transcription	Primary B cells from cord blood	blood
34	chr4:27004000-27011000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:27004200-27027200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:27004400-27006800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:27004400-27007600	Weak transcription	Gastric	stomach
38	chr4:27004800-27006800	Enhancers	Fetal Lung	lung
39	chr4:27004800-27007000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr4:27004800-27025000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr4:27005000-27007600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:27005000-27011000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:27005000-27018000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:27005000-27019400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:27005200-27006800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:27005200-27007000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:27005200-27007600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:27005200-27007600	Enhancers	NH-A	brain
49	chr4:27005200-27007800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr4:27005400-27007000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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