Variant report

Variant	rs10935340
Chromosome Location	chr3:139385396-139385397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11714276	1.00[ASW][hapmap]
rs12054405	0.89[AFR][1000 genomes]
rs12492528	1.00[YRI][hapmap]
rs17314168	1.00[YRI][hapmap]
rs2291803	1.00[YRI][hapmap]
rs4074739	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4389442	0.89[AFR][1000 genomes]
rs9790066	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[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	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10935340	RBP1	cis	cerebellum	SCAN
rs10935340	ESYT3	cis	cerebellum	SCAN
rs10935340	ADI1	trans	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139353400-139391600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:139363200-139391800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:139369800-139395200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:139371000-139389000	Weak transcription	Psoas Muscle	Psoas
5	chr3:139374200-139386800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:139374200-139394000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:139374200-139395600	Weak transcription	Gastric	stomach
8	chr3:139374400-139394600	Weak transcription	Pancreas	Pancrea
9	chr3:139374400-139394800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:139375200-139386200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:139375200-139386600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:139375200-139389400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:139375200-139390400	Weak transcription	Brain Germinal Matrix	brain
14	chr3:139375200-139390800	Weak transcription	Fetal Stomach	stomach
15	chr3:139375200-139393800	Weak transcription	Ovary	ovary
16	chr3:139375400-139385800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:139375400-139394400	Weak transcription	Brain Anterior Caudate	brain
18	chr3:139375400-139395600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:139375600-139395800	Weak transcription	Adipose Nuclei	Adipose
20	chr3:139379200-139391800	Weak transcription	Fetal Intestine Small	intestine
21	chr3:139380400-139394800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:139380800-139391600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:139381400-139391200	Weak transcription	Aorta	Aorta
24	chr3:139383200-139395600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:139384000-139394400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:139384400-139396000	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links