Variant report

Variant	rs4637173
Chromosome Location	chr2:48948856-48948857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48947110..48949799-chr2:48950949..48954085,3	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11680604	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17398267	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4374421	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4490239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55983902	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62135381	0.91[ASN][1000 genomes]
rs62135383	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62135388	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62135389	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62135390	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62135392	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62135397	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62135398	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62135399	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6714440	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6714821	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6742911	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6761185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7557060	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7559583	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567975	0.96[ASN][1000 genomes]
rs7567983	0.96[ASN][1000 genomes]
rs7571983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578785	0.96[ASN][1000 genomes]
rs7584253	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7595747	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608186	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv817851	chr2:48941428-48973127	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4637173	STON1-GTF2A1L	cis	cerebellum	SCAN
rs4637173	MCFD2	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48921600-48949600	Weak transcription	Ovary	ovary
2	chr2:48942800-48949200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:48943200-48949400	Weak transcription	Osteobl	bone
4	chr2:48943200-48950000	Weak transcription	Fetal Kidney	kidney
5	chr2:48943200-48953000	Weak transcription	K562	blood
6	chr2:48943400-48949800	Weak transcription	Fetal Stomach	stomach
7	chr2:48943400-48949800	Weak transcription	NHLF	lung
8	chr2:48943400-48955400	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:48943400-48956200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:48945400-48949600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:48945400-48955600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:48946200-48950400	Weak transcription	Fetal Lung	lung
13	chr2:48946400-48949000	Enhancers	Stomach Smooth Muscle	stomach
14	chr2:48947000-48955400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:48947200-48951600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:48947200-48956000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:48947400-48949600	Weak transcription	NH-A	brain
18	chr2:48947400-48950000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:48947400-48955800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:48947600-48956000	Weak transcription	Brain Anterior Caudate	brain
21	chr2:48947600-48956600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:48947800-48955400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:48948000-48949200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:48948000-48951800	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:48948400-48951200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:48948600-48949600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links