Variant report

Variant	rs13017297
Chromosome Location	chr2:231313327-231313328
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:231312153-231313907	GM12892	blood:	n/a	n/a
2	SPI1	chr2:231312310-231313455	GM12878	blood:	n/a	chr2:231313284-231313297 chr2:231312984-231312993
3	POLR2A	chr2:231310357-231315156	GM12892	blood:	n/a	n/a
4	POLR2A	chr2:231313286-231313935	GM12891	blood:	n/a	n/a
5	POLR2A	chr2:231311662-231313826	GM12892	blood:	n/a	n/a
6	CEBPB	chr2:231312354-231313330	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:231310306-231315168	GM12878	blood:	n/a	n/a
8	MXI1	chr2:231312486-231313383	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:231313156-231313805	GM12891	blood:	n/a	n/a
10	ATF2	chr2:231312367-231313329	GM12878	blood:	n/a	n/a
11	PML	chr2:231312198-231313384	GM12878	blood:	n/a	n/a
12	NFIC	chr2:231312134-231313477	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:231311178-231313870	GM12891	blood:	n/a	n/a
14	POLR2A	chr2:231310334-231313894	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:231313325-231313662	GM12878	blood:	n/a	n/a
16	NFIC	chr2:231312202-231313427	GM12878	blood:	n/a	n/a
17	RUNX3	chr2:231312276-231313335	GM12878	blood:	n/a	n/a
18	MTA3	chr2:231312319-231313383	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:231313324-231313424	GM12878	blood:	n/a	n/a
20	RUNX3	chr2:231312142-231313334	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SP100	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10165012	1.00[CHB][hapmap]
rs10170241	1.00[CHB][hapmap]
rs10207273	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694864	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12694866	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694868	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13000381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707444	1.00[CHB][hapmap]
rs6710287	1.00[CHB][hapmap]
rs6742304	1.00[CHB][hapmap]

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	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv584672	chr2:231289976-231348888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13017297	LOC93349	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231288800-231319000	Weak transcription	Fetal Kidney	kidney
2	chr2:231288800-231356000	Weak transcription	Stomach Mucosa	stomach
3	chr2:231301400-231314400	Weak transcription	Psoas Muscle	Psoas
4	chr2:231301800-231345000	Weak transcription	A549	lung
5	chr2:231303200-231317200	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr2:231304400-231320800	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:231306000-231314400	Weak transcription	Esophagus	oesophagus
8	chr2:231306600-231323400	Weak transcription	K562	blood
9	chr2:231306800-231318200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:231307400-231317600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:231307400-231318200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:231307400-231321800	Strong transcription	Liver	Liver
13	chr2:231307600-231315000	Strong transcription	Fetal Muscle Leg	muscle
14	chr2:231307600-231315000	Strong transcription	Left Ventricle	heart
15	chr2:231307600-231315400	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr2:231307600-231316600	Strong transcription	Primary hematopoietic stem cells	blood
17	chr2:231307600-231318200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr2:231307600-231319600	Strong transcription	Dnd41	blood
19	chr2:231307600-231336600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr2:231307800-231315000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:231307800-231315000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:231307800-231315200	Strong transcription	HSMMtube	muscle
23	chr2:231307800-231318400	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:231308000-231314000	Weak transcription	Brain Substantia Nigra	brain
25	chr2:231308000-231315000	Strong transcription	Fetal Intestine Small	intestine
26	chr2:231308000-231315200	Strong transcription	HSMM	muscle
27	chr2:231308000-231315800	Strong transcription	Placenta	Placenta
28	chr2:231308200-231315000	Strong transcription	Fetal Intestine Large	intestine
29	chr2:231308200-231316000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:231308400-231314800	Strong transcription	Gastric	stomach
31	chr2:231308400-231318000	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr2:231308600-231315000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:231308600-231318000	Strong transcription	Osteobl	bone
34	chr2:231308600-231318200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:231308800-231314600	Strong transcription	NHDF-Ad	bronchial
36	chr2:231308800-231315000	Strong transcription	NHEK	skin
37	chr2:231308800-231316200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:231308800-231316200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:231308800-231320800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:231308800-231337000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:231308800-231337400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:231309200-231313600	Strong transcription	NH-A	brain
43	chr2:231309200-231315000	Strong transcription	Fetal Stomach	stomach
44	chr2:231309200-231315000	Strong transcription	Ovary	ovary
45	chr2:231309200-231315000	Strong transcription	Pancreas	Pancrea
46	chr2:231309200-231315000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr2:231309400-231316000	Strong transcription	NHLF	lung
48	chr2:231309600-231313400	Weak transcription	Right Ventricle	heart
49	chr2:231309600-231313600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:231309600-231314200	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links