Variant report

Variant	rs6886993
Chromosome Location	chr5:16556563-16556564
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10035580	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10041159	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10053746	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10073468	0.94[ASN][1000 genomes]
rs10454940	0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12187057	0.81[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs12187879	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs1551050	0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs2162770	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2560828	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2617423	0.81[YRI][hapmap]
rs2617426	0.89[YRI][hapmap]
rs56379171	0.94[ASN][1000 genomes]
rs6860945	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[ASN][1000 genomes]
rs6862083	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882868	0.81[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs7705650	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7730689	0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs9312921	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9312922	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881187	chr5:16514269-16654960	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6886993	FAM134B	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16522400-16567400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:16542600-16567200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr5:16543200-16591600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:16543600-16589800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:16544000-16562400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr5:16544200-16565200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr5:16545000-16574600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr5:16546200-16559400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr5:16549200-16569000	Weak transcription	Left Ventricle	heart
10	chr5:16549200-16580200	Weak transcription	Gastric	stomach
11	chr5:16550400-16556800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:16550400-16557400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:16552400-16559200	Weak transcription	Primary T cells from cord blood	blood
14	chr5:16553000-16568600	Weak transcription	NHDF-Ad	bronchial
15	chr5:16553000-16573400	Weak transcription	Fetal Intestine Small	intestine
16	chr5:16553200-16556800	Weak transcription	Brain Angular Gyrus	brain
17	chr5:16553200-16557200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:16553200-16562000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr5:16553200-16564600	Weak transcription	Psoas Muscle	Psoas
20	chr5:16553200-16564600	Weak transcription	Thymus	Thymus
21	chr5:16553400-16556600	Weak transcription	Brain Substantia Nigra	brain
22	chr5:16553400-16556800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:16553400-16558200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:16553400-16559200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:16553400-16559600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:16553400-16564200	Weak transcription	Fetal Heart	heart
27	chr5:16553400-16569600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr5:16553400-16572800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr5:16553600-16559200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:16554200-16556800	Weak transcription	Brain Hippocampus Middle	brain
31	chr5:16554400-16556600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:16555200-16571400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:16555400-16556600	Enhancers	Primary B cells from peripheral blood	blood
34	chr5:16555600-16558200	Weak transcription	Brain Anterior Caudate	brain
35	chr5:16556400-16556600	Enhancers	Fetal Thymus	thymus
36	chr5:16556400-16569600	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links