Variant report

Variant	rs12613263
Chromosome Location	chr2:96863677-96863678
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr2:96863610-96863928	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr2:96863324-96863929	HUVEC	blood vessel:	n/a	n/a
3	FOS	chr2:96863665-96863923	MCF10A-Er-Src	breast:	n/a	n/a
4	JUN	chr2:96863541-96863793	K562	blood:	n/a	n/a
5	POLR2A	chr2:96863278-96865840	HepG2	liver:	n/a	n/a
6	FOS	chr2:96863385-96863873	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr2:96863563-96863763	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr2:96863359-96863971	MCF10A-Er-Src	breast:	n/a	n/a
9	JUND	chr2:96863468-96863951	K562	blood:	n/a	n/a
10	ARID3A	chr2:96863321-96863866	K562	blood:	n/a	n/a
11	POLR2A	chr2:96863286-96863852	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:96860049..96862444-chr2:96862916..96864839,3	K562	blood:
2	chr2:96863176..96865884-chr2:96930469..96932067,2	MCF-7	breast:
3	chr2:96863187..96864972-chr2:96888202..96890983,2	K562	blood:
4	chr2:96862732..96864612-chr2:96933173..96934680,2	K562	blood:
5	chr2:96856407..96858673-chr2:96862043..96864010,2	MCF-7	breast:
6	chr2:96849014..96850670-chr2:96863133..96864730,2	K562	blood:

No data

Variant related genes	Relation type
STARD7	TF binding region
ENSG00000084090	Chromatin interaction
ENSG00000135956	Chromatin interaction
ENSG00000144021	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11551400	0.83[EUR][1000 genomes]
rs12617019	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12618133	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276650	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852673	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4371393	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4592891	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4826	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57476471	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59082429	0.81[EUR][1000 genomes]
rs59664047	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62153010	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62153011	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62153014	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153018	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62153020	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62153022	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62153029	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72825854	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72825856	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72825864	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72825877	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7579709	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7580178	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs997548	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS 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 miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3435047	chr2:96836850-96890437	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12613263	CIAO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96849600-96872600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:96849800-96871000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:96851000-96869400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:96859000-96865800	Weak transcription	Esophagus	oesophagus
5	chr2:96859000-96866000	Weak transcription	Gastric	stomach
6	chr2:96859000-96866400	Weak transcription	Pancreas	Pancrea
7	chr2:96859000-96867800	Weak transcription	Spleen	Spleen
8	chr2:96859000-96870800	Weak transcription	Fetal Brain Male	brain
9	chr2:96859000-96870800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:96859000-96873200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:96860200-96863800	Weak transcription	Small Intestine	intestine
12	chr2:96860200-96865800	Weak transcription	Ovary	ovary
13	chr2:96860200-96869400	Weak transcription	Aorta	Aorta
14	chr2:96860200-96871200	Weak transcription	Fetal Kidney	kidney
15	chr2:96860600-96867800	Weak transcription	Fetal Lung	lung
16	chr2:96860800-96865400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:96861000-96865000	Weak transcription	Adipose Nuclei	Adipose
18	chr2:96861000-96866000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:96861000-96866600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:96861000-96871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:96861200-96863800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:96861200-96864200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:96861200-96865200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:96861200-96865400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:96861200-96865400	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:96861200-96865800	Weak transcription	Lung	lung
27	chr2:96861200-96867200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:96861200-96867800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:96861200-96867800	Weak transcription	Brain Germinal Matrix	brain
30	chr2:96861200-96868000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:96861200-96868000	Weak transcription	HSMMtube	muscle
32	chr2:96861200-96869600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:96861200-96869800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:96861400-96863800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:96861400-96864000	Weak transcription	Primary B cells from cord blood	blood
36	chr2:96861400-96864000	Weak transcription	Brain Angular Gyrus	brain
37	chr2:96861400-96864200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr2:96861400-96864200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr2:96861400-96864200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:96861400-96864200	Weak transcription	Brain Anterior Caudate	brain
41	chr2:96861400-96864200	Weak transcription	GM12878-XiMat	blood
42	chr2:96861400-96864400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:96861400-96864600	Weak transcription	Hela-S3	cervix
44	chr2:96861400-96864800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:96861400-96864800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:96861400-96864800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr2:96861400-96864800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr2:96861400-96865200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr2:96861400-96865400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:96861400-96865800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links