Variant report

Variant	rs12613508
Chromosome Location	chr2:85700178-85700179
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
2	chr2:85697443..85708380-chr2:85764609..85769775,19	K562	blood:
3	chr2:85695182..85700475-chr2:85771258..85775492,7	K562	blood:
4	chr2:85699337..85700838-chr2:85763015..85764537,2	K562	blood:
5	chr2:85695571..85701406-chr2:85763524..85768199,9	MCF-7	breast:
6	chr2:85671604..85674424-chr2:85697092..85700919,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168906	Chromatin interaction
ENSG00000266577	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000115486	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10196697	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126994	0.84[ASN][1000 genomes]
rs11673725	0.81[ASN][1000 genomes]
rs11883636	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1470501	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4993939	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4993940	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6714421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7577642	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
3	nsv834283	chr2:85609500-85755708	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12613508	IMMT	cis	cerebellum	SCAN
rs12613508	MRPL35	cis	parietal	SCAN
rs12613508	REEP1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85693400-85701400	Enhancers	Fetal Intestine Small	intestine
2	chr2:85694400-85700600	Enhancers	Fetal Intestine Large	intestine
3	chr2:85695200-85700800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:85696200-85703200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:85696400-85702800	Weak transcription	Left Ventricle	heart
6	chr2:85696400-85703200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:85697600-85700800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:85697600-85700800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:85698000-85700800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:85698400-85700400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:85698600-85700200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr2:85698600-85703000	Weak transcription	Colonic Mucosa	Colon
13	chr2:85698600-85705600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:85698800-85701000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:85698800-85703200	Weak transcription	Adipose Nuclei	Adipose
16	chr2:85699000-85700800	Enhancers	NHEK	skin
17	chr2:85699000-85701600	Enhancers	HepG2	liver
18	chr2:85699000-85702400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:85699000-85703000	Weak transcription	Small Intestine	intestine
20	chr2:85699400-85700200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr2:85699400-85700400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:85699400-85700400	Weak transcription	Pancreas	Pancrea
23	chr2:85699400-85702400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:85699400-85703000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:85699400-85703000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:85699400-85703000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:85699400-85703000	Weak transcription	Osteobl	bone
28	chr2:85699400-85703200	Weak transcription	Esophagus	oesophagus
29	chr2:85699400-85703200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:85699600-85701400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:85699600-85702600	Weak transcription	Liver	Liver
32	chr2:85699800-85700800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr2:85699800-85703000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:85699800-85703000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:85699800-85703000	Weak transcription	HSMM	muscle
36	chr2:85699800-85703200	Weak transcription	A549	lung
37	chr2:85700000-85703200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:85700000-85703200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:85700000-85703200	Weak transcription	HMEC	breast

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