Variant report

Variant	rs13395691
Chromosome Location	chr2:113335619-113335620
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113297854..113299874-chr2:113334831..113337055,2	K562	blood:
2	chr2:113332582..113336082-chr2:113340503..113343109,3	K562	blood:
3	chr2:113297854..113301606-chr2:113334028..113336907,4	K562	blood:

Variant related genes	Relation type
ENSG00000125630	Chromatin interaction
ENSG00000125611	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10169290	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10169344	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10183849	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10200067	0.81[ASN][1000 genomes]
rs10205187	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469608	0.81[JPT][hapmap]
rs13395779	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13412193	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.90[ASN][1000 genomes]
rs13413001	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13424021	0.87[ASN][1000 genomes]
rs1583616	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2241804	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34179430	0.81[JPT][hapmap]
rs3748026	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3789724	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.90[ASN][1000 genomes]
rs3961914	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57339041	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59033131	0.90[ASN][1000 genomes]
rs60489148	0.90[ASN][1000 genomes]
rs60518507	0.89[ASN][1000 genomes]
rs61669219	0.90[ASN][1000 genomes]
rs62158580	0.81[ASN][1000 genomes]
rs62158582	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62158584	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62158585	0.90[ASN][1000 genomes]
rs62158586	0.90[ASN][1000 genomes]
rs62158591	0.93[ASN][1000 genomes]
rs62158643	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62158644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7559710	0.81[JPT][hapmap]
rs7565714	0.87[JPT][hapmap]
rs7576952	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs9308672	0.90[ASN][1000 genomes]
rs9808491	0.90[ASN][1000 genomes]

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	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats 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	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13395691	POLR1B	cis	Artery Tibial	GTEx
rs13395691	POLR1B	cis	Stomach	GTEx
rs13395691	POLR1B	cis	Esophagus Muscularis	GTEx
rs13395691	POLR1B	cis	Thyroid	GTEx
rs13395691	POLR1B	cis	Nerve Tibial	GTEx
rs13395691	POLR1B	cis	Adipose Subcutaneous	GTEx
rs13395691	POLR1B	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113301200-113340200	Weak transcription	Right Atrium	heart
2	chr2:113301200-113341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:113326400-113340200	Weak transcription	Stomach Mucosa	stomach
4	chr2:113326600-113341000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:113330400-113339800	Weak transcription	Fetal Heart	heart
6	chr2:113331400-113336000	Strong transcription	HMEC	breast
7	chr2:113331400-113340800	Weak transcription	Fetal Brain Male	brain
8	chr2:113331400-113341400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:113332200-113341600	Weak transcription	Small Intestine	intestine
10	chr2:113333000-113340800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:113333000-113341000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:113333200-113339800	Weak transcription	Pancreas	Pancrea
13	chr2:113333200-113341000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:113333200-113341000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:113333200-113341000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:113333200-113341000	Weak transcription	Fetal Kidney	kidney
17	chr2:113333200-113341200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:113333200-113341200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:113333200-113341200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:113333200-113341200	Weak transcription	Lung	lung
21	chr2:113333400-113340200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:113333400-113340800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:113333400-113341000	Weak transcription	Spleen	Spleen
24	chr2:113333600-113341000	Weak transcription	Gastric	stomach
25	chr2:113333600-113341400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:113333800-113336200	Weak transcription	Fetal Brain Female	brain
27	chr2:113333800-113340200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr2:113333800-113340800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:113333800-113341000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:113333800-113341000	Weak transcription	Right Ventricle	heart
31	chr2:113334000-113336400	Weak transcription	Hela-S3	cervix
32	chr2:113334000-113336400	Weak transcription	HUVEC	blood vessel
33	chr2:113334000-113336800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:113334000-113339800	Weak transcription	K562	blood
35	chr2:113334000-113340200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:113334000-113340200	Weak transcription	Adipose Nuclei	Adipose
37	chr2:113334000-113340200	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:113334000-113340800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:113334000-113341000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:113334200-113336600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:113334200-113336800	Weak transcription	NH-A	brain
42	chr2:113334200-113339800	Weak transcription	Brain Substantia Nigra	brain
43	chr2:113334200-113340200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:113334200-113340400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr2:113334200-113340800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:113334200-113340800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:113334200-113340800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:113334200-113340800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:113334200-113341000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:113334200-113341200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links