Variant report

Variant	rs2472153
Chromosome Location	chr10:38303815-38303816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:38298520..38302373-chr10:38302869..38306244,5	K562	blood:

Variant related genes	Relation type
ENSG00000189180	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1208578	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1208619	0.81[EUR][1000 genomes]
rs1208621	0.87[EUR][1000 genomes]
rs12413083	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12414618	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1735625	0.86[EUR][1000 genomes]
rs17608725	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176831	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176832	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176890	0.88[CEU][hapmap]
rs1779073	0.89[EUR][1000 genomes]
rs1854562	0.88[CEU][hapmap]
rs200907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs200909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs200913	0.81[EUR][1000 genomes]
rs200944	0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2021651	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2178958	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293962	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2472159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2472160	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs2474545	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2474553	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2480521	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2489166	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2504137	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505218	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2738221	0.89[EUR][1000 genomes]
rs2753883	0.84[EUR][1000 genomes]
rs664543	0.85[EUR][1000 genomes]
rs677565	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7088655	0.88[CEU][hapmap]
rs766362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7895468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9418311	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv534122	chr10:38240258-38356008	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv540566	chr10:38301001-38680127	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv947853	chr10:38301938-38306401	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2472153	ZNF37A	Cis_1M	lymphoblastoid	RTeQTL
rs2472153	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38300400-38304200	Weak transcription	Esophagus	oesophagus
2	chr10:38300400-38305200	Weak transcription	Lung	lung
3	chr10:38300400-38305800	Weak transcription	Ovary	ovary
4	chr10:38300400-38305800	Weak transcription	Spleen	Spleen
5	chr10:38300400-38306000	Weak transcription	Small Intestine	intestine
6	chr10:38300400-38319600	Weak transcription	Gastric	stomach
7	chr10:38300600-38304000	Weak transcription	Aorta	Aorta
8	chr10:38300600-38305200	Weak transcription	Left Ventricle	heart
9	chr10:38300600-38306000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:38300600-38306000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr10:38300600-38318000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr10:38300600-38331600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:38300600-38336000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr10:38300600-38339400	Weak transcription	Psoas Muscle	Psoas
15	chr10:38300800-38304200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:38300800-38304600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr10:38300800-38305600	Weak transcription	NHDF-Ad	bronchial
18	chr10:38300800-38306200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:38300800-38306600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr10:38300800-38307000	Weak transcription	Colonic Mucosa	Colon
21	chr10:38300800-38307200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr10:38300800-38307600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr10:38300800-38308600	Weak transcription	HSMM	muscle
24	chr10:38300800-38322000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr10:38300800-38339200	Weak transcription	HSMMtube	muscle
26	chr10:38301000-38304000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr10:38301000-38304800	Weak transcription	Brain Hippocampus Middle	brain
28	chr10:38301000-38305000	Weak transcription	Brain Angular Gyrus	brain
29	chr10:38301000-38305200	Weak transcription	Osteobl	bone
30	chr10:38301000-38305800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr10:38301000-38306000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr10:38301200-38304000	Weak transcription	Thymus	Thymus
33	chr10:38301200-38304400	Weak transcription	NH-A	brain
34	chr10:38301200-38304600	Weak transcription	HMEC	breast
35	chr10:38301200-38304600	Weak transcription	NHEK	skin
36	chr10:38301200-38304800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr10:38301200-38304800	Weak transcription	Brain Substantia Nigra	brain
38	chr10:38301200-38304800	Weak transcription	Colon Smooth Muscle	Colon
39	chr10:38301200-38304800	Weak transcription	HUVEC	blood vessel
40	chr10:38301200-38305000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr10:38301200-38305200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr10:38301200-38306000	Weak transcription	Right Ventricle	heart
43	chr10:38301200-38306400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr10:38301200-38307200	Weak transcription	Stomach Mucosa	stomach
45	chr10:38301200-38308400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr10:38301200-38308600	Weak transcription	Fetal Heart	heart
47	chr10:38301200-38311200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr10:38301200-38320400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr10:38301200-38325000	Weak transcription	NHLF	lung
50	chr10:38301400-38305200	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links