Variant report

Variant	rs10197948
Chromosome Location	chr2:37805146-37805147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37804698..37807657-chr2:37813185..37814836,2	K562	blood:
2	chr2:37795029..37797811-chr2:37802354..37805859,3	K562	blood:
3	chr2:37782232..37784356-chr2:37804122..37805641,2	MCF-7	breast:
4	chr2:37789729..37791788-chr2:37804945..37807693,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10168778	0.83[EUR][1000 genomes]
rs10173816	0.90[EUR][1000 genomes]
rs10176881	0.84[EUR][1000 genomes]
rs10184801	0.99[EUR][1000 genomes]
rs10208172	0.99[EUR][1000 genomes]
rs11124592	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11687796	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887848	0.85[EUR][1000 genomes]
rs12612951	0.85[EUR][1000 genomes]
rs35422160	0.84[EUR][1000 genomes]
rs35574342	0.85[EUR][1000 genomes]
rs4670208	0.87[EUR][1000 genomes]
rs4670730	0.87[EUR][1000 genomes]
rs6544093	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6708088	0.90[EUR][1000 genomes]
rs6712065	0.84[EUR][1000 genomes]
rs6730320	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6733354	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6733496	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747152	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs740992	0.90[EUR][1000 genomes]
rs7557304	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7560890	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7564992	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7587009	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs765372	0.99[EUR][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	nsv833814	chr2:37643132-37840247	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv456374	chr2:37669487-37868214	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv470453	chr2:37669487-37868214	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv581473	chr2:37669487-37868214	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription 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	14 gene(s)	inside rSNPs	diseases
6	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	esv2762494	chr2:37802996-37813373	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10197948	CDC42EP3	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37796400-37809600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:37796600-37810200	Weak transcription	Pancreas	Pancrea
3	chr2:37798600-37806400	Weak transcription	K562	blood
4	chr2:37799200-37812400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:37801400-37807600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:37801600-37806200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:37801600-37809600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:37802000-37812400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:37803600-37805200	Enhancers	HMEC	breast
10	chr2:37804400-37805800	Weak transcription	NHDF-Ad	bronchial
11	chr2:37804400-37806400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:37804400-37809400	Weak transcription	Primary T cells from cord blood	blood
13	chr2:37804600-37806000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:37804600-37809800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:37804600-37810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:37804600-37810200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:37804600-37810200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:37804800-37806200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:37804800-37808800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:37804800-37809400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:37804800-37809600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:37804800-37809600	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links