Variant report

Variant	rs6737227
Chromosome Location	chr2:55460605-55460606
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10200120	0.87[ASN][1000 genomes]
rs1056445	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11125559	0.80[YRI][hapmap]
rs11357	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12052613	0.85[ASN][1000 genomes]
rs17852670	0.82[AMR][1000 genomes]
rs2043712	0.86[YRI][hapmap]
rs2576711	0.91[JPT][hapmap]
rs2576712	0.85[ASN][1000 genomes]
rs2589080	0.86[ASN][1000 genomes]
rs2589092	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2589093	0.87[ASN][1000 genomes]
rs2589094	1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2589096	0.91[JPT][hapmap]
rs2589100	0.84[ASN][1000 genomes]
rs2864819	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2864826	0.84[ASN][1000 genomes]
rs2917779	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2920967	0.84[ASN][1000 genomes]
rs34348115	0.82[CEU][hapmap];0.95[YRI][hapmap]
rs4435493	0.91[CHB][hapmap];0.82[AMR][1000 genomes]
rs55997390	0.84[ASN][1000 genomes]
rs6545480	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6755515	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72799507	0.85[ASN][1000 genomes]
rs7597293	0.84[ASN][1000 genomes]
rs934709	0.90[CHB][hapmap];0.82[AMR][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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6737227	CLHC1	cis	Artery Aorta	GTEx
rs6737227	CLHC1	cis	Artery Tibial	GTEx
rs6737227	CLHC1	cis	Whole Blood	GTEx
rs6737227	CLHC1	cis	Adipose Subcutaneous	GTEx
rs6737227	CLHC1	cis	Nerve Tibial	GTEx
rs6737227	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs6737227	CLHC1	cis	Esophagus Muscularis	GTEx
rs6737227	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs6737227	C2orf63	cis	multi-tissue	Pritchard
rs6737227	CLHC1	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55458200-55460800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:55458200-55460800	Active TSS	HMEC	breast
3	chr2:55458400-55460800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:55458400-55460800	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr2:55458400-55460800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:55458400-55460800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:55458400-55460800	Active TSS	Fetal Kidney	kidney
8	chr2:55458400-55460800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr2:55458400-55461400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:55458600-55460800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:55458600-55460800	Active TSS	Fetal Intestine Large	intestine
12	chr2:55458600-55460800	Active TSS	Fetal Intestine Small	intestine
13	chr2:55458600-55460800	Active TSS	Left Ventricle	heart
14	chr2:55458600-55460800	Active TSS	Lung	lung
15	chr2:55458600-55460800	Active TSS	Ovary	ovary
16	chr2:55458600-55460800	Active TSS	Pancreas	Pancrea
17	chr2:55458600-55460800	Active TSS	Right Ventricle	heart
18	chr2:55458600-55460800	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr2:55458600-55461200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:55458600-55461200	Active TSS	HSMMtube	muscle
21	chr2:55458600-55462200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:55458800-55460800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:55458800-55460800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:55458800-55460800	Active TSS	Gastric	stomach
25	chr2:55458800-55461000	Active TSS	Esophagus	oesophagus
26	chr2:55458800-55461000	Bivalent/Poised TSS	HepG2	liver
27	chr2:55458800-55461000	Active TSS	NHDF-Ad	bronchial
28	chr2:55458800-55461400	Active TSS	Psoas Muscle	Psoas
29	chr2:55459000-55460800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:55459000-55460800	Active TSS	Rectal Smooth Muscle	rectum
31	chr2:55459000-55461200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
32	chr2:55459200-55460800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:55459200-55461600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:55459800-55461800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
35	chr2:55459800-55462000	Transcr. at gene 5' and 3'	Dnd41	blood
36	chr2:55460000-55461000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr2:55460000-55461000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr2:55460000-55461000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:55460000-55462400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
40	chr2:55460000-55463000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
41	chr2:55460000-55463400	Transcr. at gene 5' and 3'	K562	blood
42	chr2:55460200-55460800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:55460200-55460800	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr2:55460200-55461000	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr2:55460200-55461200	Transcr. at gene 5' and 3'	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:55460200-55461400	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr2:55460200-55462000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
48	chr2:55460200-55462200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:55460200-55462600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
50	chr2:55460200-55463000	Transcr. at gene 5' and 3'	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links