Variant report

Variant	rs11140010
Chromosome Location	chr9:85912228-85912229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:85910928..85912509-chr9:85920492..85923421,2	K562	blood:
2	chr9:85910411..85912906-chr9:85925285..85927422,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172159	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10867979	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11139998	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs11140001	0.86[CHB][hapmap]
rs11140009	0.83[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1323778	0.85[CHB][hapmap];0.91[ASN][1000 genomes]
rs1323779	0.91[ASN][1000 genomes]
rs1323782	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs1323785	0.85[CHB][hapmap]
rs17086124	0.85[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs55707933	0.82[ASN][1000 genomes]
rs6559718	0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7034332	0.87[CHD][hapmap]
rs7856762	0.85[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046491	chr9:85861492-86063992	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv6586	chr9:85869828-85914812	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11140010	RASEF	cis	parietal	SCAN
rs11140010	NTRK2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85866200-85913000	Weak transcription	Aorta	Aorta
2	chr9:85884200-85912400	Weak transcription	HepG2	liver
3	chr9:85895000-85912800	Weak transcription	Fetal Brain Female	brain
4	chr9:85896000-85913600	Weak transcription	Psoas Muscle	Psoas
5	chr9:85896000-85919800	Weak transcription	Lung	lung
6	chr9:85896400-85912600	Weak transcription	Gastric	stomach
7	chr9:85896400-85913400	Weak transcription	Brain Germinal Matrix	brain
8	chr9:85896600-85913000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr9:85896800-85922800	Weak transcription	Spleen	Spleen
10	chr9:85897000-85912600	Weak transcription	Adipose Nuclei	Adipose
11	chr9:85897000-85912600	Weak transcription	Ovary	ovary
12	chr9:85897000-85912800	Weak transcription	Right Ventricle	heart
13	chr9:85897200-85913000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr9:85897200-85919200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:85897200-85922000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:85897400-85914800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:85905800-85919000	Weak transcription	Fetal Stomach	stomach
18	chr9:85906400-85915000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:85906600-85919400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr9:85906800-85919600	Weak transcription	Pancreas	Pancrea
21	chr9:85908400-85913000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:85908400-85913800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:85908800-85913000	Weak transcription	Fetal Muscle Leg	muscle
24	chr9:85909000-85914200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:85909000-85918400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:85909200-85928000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:85910000-85913600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:85910400-85918000	Weak transcription	Fetal Brain Male	brain
29	chr9:85910600-85914000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr9:85910800-85914000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr9:85911400-85913200	Weak transcription	Fetal Intestine Small	intestine
32	chr9:85911400-85918800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr9:85911600-85912800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr9:85911600-85914000	Strong transcription	Left Ventricle	heart
35	chr9:85912000-85913600	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:85912200-85915200	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links