Variant report

Variant	rs2183995
Chromosome Location	chr1:62479403-62479404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11207894	0.84[ASN][1000 genomes]
rs11586551	0.82[ASN][1000 genomes]
rs12073709	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12076492	0.86[CHB][hapmap];0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs12083806	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12084203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17122904	0.82[CHB][hapmap]
rs17122931	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs58541070	0.92[ASN][1000 genomes]
rs7556298	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv546416	chr1:62437872-62492215	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2183995	CLTA	trans	parietal	SCAN
rs2183995	ATG4C	cis	cerebellum	SCAN
rs2183995	L1TD1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
2	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
3	chr1:62424200-62494200	Weak transcription	Esophagus	oesophagus
4	chr1:62446600-62487600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:62447400-62481200	Weak transcription	Lung	lung
6	chr1:62458800-62521400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:62459000-62484000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:62459000-62516000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:62459200-62487800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:62459200-62511200	Weak transcription	Gastric	stomach
12	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:62459400-62484000	Weak transcription	Liver	Liver
14	chr1:62459400-62493800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:62459600-62483600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:62459600-62494200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:62459800-62483600	Weak transcription	NHEK	skin
18	chr1:62460000-62499600	Weak transcription	Fetal Intestine Large	intestine
19	chr1:62460000-62516400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:62460200-62487600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:62460200-62516000	Weak transcription	HMEC	breast
23	chr1:62466400-62494200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:62469000-62533600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:62469800-62488000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:62473000-62488200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:62473800-62487000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:62474200-62518600	Weak transcription	Primary T cells from cord blood	blood
29	chr1:62478600-62479600	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:62478600-62480000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:62479000-62482400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:62479000-62482800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:62479000-62487600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:62479200-62480600	Strong transcription	Fetal Intestine Small	intestine
35	chr1:62479200-62485200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:62479400-62483800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:62479400-62485600	Weak transcription	Ovary	ovary
38	chr1:62479400-62488200	Weak transcription	Psoas Muscle	Psoas
39	chr1:62479400-62490200	Weak transcription	Left Ventricle	heart
40	chr1:62479400-62490200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:62479400-62493600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:62479400-62496000	Weak transcription	Fetal Kidney	kidney

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