Variant report

Variant	rs10955140
Chromosome Location	chr8:99014550-99014551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:99006609..99009034-chr8:99014356..99016713,2	MCF-7	breast:
2	chr8:98880331..98882636-chr8:99012826..99014648,3	MCF-7	breast:
3	chr8:98852045..98852568-chr8:99013936..99014703,2	MCF-7	breast:
4	chr8:99014119..99017352-chr8:99021059..99024142,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132561	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10106983	0.87[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs10955141	0.85[CEU][hapmap]
rs10955143	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10955144	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10955146	0.85[CEU][hapmap]
rs11776602	0.85[CEU][hapmap]
rs11784449	0.85[CEU][hapmap]
rs11785807	0.85[CEU][hapmap]
rs12549307	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12676252	0.86[CHB][hapmap];0.95[ASN][1000 genomes]
rs13254615	0.85[CEU][hapmap]
rs13254737	0.85[CEU][hapmap]
rs13270713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13439743	0.84[CEU][hapmap]
rs2034780	0.93[CHB][hapmap];0.82[JPT][hapmap];0.98[ASN][1000 genomes]
rs2290469	0.85[CEU][hapmap]
rs36191777	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4735521	0.93[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.98[ASN][1000 genomes]
rs6985434	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6986891	0.85[CEU][hapmap]
rs6987112	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv528695	chr8:98960813-99022009	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10955140	GRHL2	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:98992600-99019400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr8:98994200-99014800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr8:99008200-99015400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr8:99008400-99045000	Weak transcription	Colonic Mucosa	Colon
5	chr8:99008800-99014800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr8:99009000-99016800	Weak transcription	Placenta	Placenta
7	chr8:99009000-99030000	Weak transcription	Pancreas	Pancrea
8	chr8:99009000-99030200	Weak transcription	Esophagus	oesophagus
9	chr8:99009600-99022600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr8:99009800-99014600	Weak transcription	Right Atrium	heart
11	chr8:99010000-99015400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr8:99011800-99015200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr8:99012000-99017200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr8:99012000-99028800	Weak transcription	Aorta	Aorta
15	chr8:99012000-99032000	Weak transcription	Gastric	stomach
16	chr8:99012400-99028800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr8:99013400-99015000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:99013400-99015000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr8:99013400-99015400	Enhancers	Brain Angular Gyrus	brain
20	chr8:99013600-99014800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr8:99013600-99015000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:99013800-99014800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr8:99013800-99015600	Enhancers	Brain Anterior Caudate	brain
24	chr8:99013800-99018600	Weak transcription	Fetal Intestine Small	intestine
25	chr8:99014000-99014600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr8:99014000-99014800	Enhancers	Adipose Nuclei	Adipose
27	chr8:99014000-99014800	Enhancers	Colon Smooth Muscle	Colon
28	chr8:99014000-99015000	Enhancers	NHLF	lung
29	chr8:99014000-99015000	Enhancers	Osteobl	bone
30	chr8:99014000-99015200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr8:99014000-99022400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr8:99014200-99014600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr8:99014200-99014600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr8:99014200-99014600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr8:99014200-99014600	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr8:99014200-99014600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr8:99014200-99014600	Enhancers	Stomach Smooth Muscle	stomach
38	chr8:99014200-99014600	Enhancers	HSMM	muscle
39	chr8:99014200-99014800	Enhancers	Fetal Stomach	stomach
40	chr8:99014200-99014800	Enhancers	Ovary	ovary
41	chr8:99014200-99014800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
42	chr8:99014200-99014800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr8:99014200-99014800	Enhancers	NH-A	brain
44	chr8:99014200-99015000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr8:99014200-99015000	Enhancers	HUVEC	blood vessel
46	chr8:99014200-99015000	Enhancers	NHDF-Ad	bronchial
47	chr8:99014200-99015400	Enhancers	Brain Substantia Nigra	brain
48	chr8:99014200-99025400	Genic enhancers	Fetal Muscle Leg	muscle
49	chr8:99014200-99029600	Weak transcription	Fetal Intestine Large	intestine
50	chr8:99014400-99014600	Enhancers	Liver	Liver

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