Variant report

Variant	rs6990134
Chromosome Location	chr8:8915949-8915950
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1016512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1045527	1.00[CHD][hapmap]
rs1045528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10503395	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13249731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13250674	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13250919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13258661	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13260103	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13261370	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13263480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13271797	1.00[CHD][hapmap]
rs13273769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13273871	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13274157	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13276286	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13276537	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13281029	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430931	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17155162	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044389	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28393746	0.95[EUR][1000 genomes]
rs28516774	0.86[EUR][1000 genomes]
rs28534948	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28812315	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2956245	0.80[EUR][1000 genomes]
rs34111588	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34334157	0.84[EUR][1000 genomes]
rs34391124	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34412730	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34418902	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34712023	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34752993	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34854114	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35227233	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35616716	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35808561	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3958881	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4841088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4841092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55634245	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55696609	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66483157	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66869483	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67139167	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67259528	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67434672	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67575865	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67958495	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs68043139	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6985908	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6989707	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6993811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6994214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6994551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7008080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7012302	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71514525	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71514527	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73195799	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73197711	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73197712	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7387683	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7816149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7816450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9650616	1.00[CHD][hapmap]
rs9650628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6990134	PPP1R3B	cis	parietal	SCAN
rs6990134	THEX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8899000-8919200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:8913600-8916400	Enhancers	Fetal Intestine Large	intestine
3	chr8:8914400-8916000	Enhancers	Ovary	ovary
4	chr8:8914600-8916000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr8:8914600-8916000	Enhancers	Fetal Muscle Leg	muscle
6	chr8:8914600-8916000	Enhancers	Placenta	Placenta
7	chr8:8914600-8916200	Enhancers	Fetal Intestine Small	intestine
8	chr8:8914600-8916200	Enhancers	NHLF	lung
9	chr8:8914600-8917000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr8:8914800-8916000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:8914800-8916000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr8:8914800-8916000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr8:8914800-8916000	Enhancers	Fetal Stomach	stomach
14	chr8:8914800-8916000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr8:8914800-8916200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr8:8914800-8916200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr8:8914800-8916200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr8:8914800-8916200	Enhancers	Fetal Lung	lung
19	chr8:8914800-8916200	Enhancers	NH-A	brain
20	chr8:8914800-8916400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr8:8915000-8916000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr8:8915000-8916200	Enhancers	Placenta Amnion	Placenta Amnion
23	chr8:8915000-8916400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr8:8915000-8916400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr8:8915000-8916400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr8:8915000-8923600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr8:8915200-8916000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr8:8915200-8916000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr8:8915200-8916000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr8:8915200-8916000	Enhancers	Brain Germinal Matrix	brain
31	chr8:8915200-8916000	Flanking Active TSS	HSMM	muscle
32	chr8:8915200-8916000	Flanking Active TSS	HSMMtube	muscle
33	chr8:8915200-8916200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr8:8915200-8916200	Enhancers	K562	blood
35	chr8:8915200-8916200	Flanking Active TSS	NHDF-Ad	bronchial
36	chr8:8915400-8916000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr8:8915400-8916000	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr8:8915400-8916200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr8:8915400-8916200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr8:8915400-8916200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr8:8915400-8916200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr8:8915400-8916200	Enhancers	HepG2	liver
43	chr8:8915400-8928000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr8:8915600-8916000	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr8:8915600-8916600	Enhancers	Fetal Heart	heart
46	chr8:8915800-8916000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr8:8915800-8916000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr8:8915800-8916000	Enhancers	Osteobl	bone
49	chr8:8915800-8916200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr8:8915800-8916200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links