Variant report

Variant	rs6746998
Chromosome Location	chr2:208929601-208929602
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	chr2:208926513..208930859-chr2:208931530..208934190,4	K562	blood:
2	chr2:208914228..208916242-chr2:208929197..208930926,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10932231	1.00[ASN][1000 genomes]
rs10932232	0.97[ASN][1000 genomes]
rs10932233	0.98[ASN][1000 genomes]
rs10932238	0.89[ASN][1000 genomes]
rs11681747	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11683477	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11694118	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11892539	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11892554	0.85[CEU][hapmap];0.85[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11894673	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11896152	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11896248	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12465847	0.86[ASN][1000 genomes]
rs12987978	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16840404	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17538082	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2123296	0.89[ASN][1000 genomes]
rs34100088	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35306034	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4234085	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4287753	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4673378	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4675729	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4675730	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4675731	0.89[ASN][1000 genomes]
rs62192797	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6711974	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6723206	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6727089	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6727122	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6735060	0.89[ASN][1000 genomes]
rs7422654	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7422655	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs896637	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6746998	FZD5	cis	parietal	SCAN
rs6746998	PLEKHM3	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208928400-208929800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:208928600-208929800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:208928600-208929800	Enhancers	Osteobl	bone
4	chr2:208928800-208929800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:208928800-208929800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:208928800-208929800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:208928800-208929800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:208928800-208929800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr2:208928800-208929800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:208928800-208929800	Enhancers	HSMM	muscle
11	chr2:208928800-208929800	Enhancers	NH-A	brain
12	chr2:208928800-208929800	Enhancers	NHDF-Ad	bronchial
13	chr2:208928800-208929800	Enhancers	NHLF	lung
14	chr2:208928800-208930400	Weak transcription	Fetal Brain Male	brain
15	chr2:208929000-208929800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr2:208929000-208929800	Enhancers	HSMMtube	muscle
17	chr2:208929200-208929800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:208929200-208929800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:208929200-208929800	Enhancers	NHEK	skin
20	chr2:208929200-208930600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:208929200-208930600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:208929200-208931000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:208929600-208929800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:208929600-208929800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:208929600-208929800	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links