Variant report

Variant	rs10494163
Chromosome Location	chr1:114520712-114520713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:114518336-114522222	K562	blood:	n/a	n/a
2	POLR2A	chr1:114520582-114520814	GM12891	blood:	n/a	n/a
3	EP300	chr1:114520302-114522674	SK-N-SH	brain:	n/a	chr1:114521337-114521351 chr1:114521336-114521350 chr1:114521983-114521997

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114506613..114508905-chr1:114518738..114521439,2	MCF-7	breast:
2	chr1:114519974..114522024-chr16:67185216..67187500,2	MCF-7	breast:
3	chr1:114519675..114522268-chr16:67207435..67209406,2	MCF-7	breast:
4	chr1:114520426..114521090-chr1:115101014..115101813,2	MCF-7	breast:
5	chr1:114519574..114521324-chr16:67217979..67220821,2	MCF-7	breast:
6	chr1:114517866..114521234-chr1:114758267..114762290,4	MCF-7	breast:
7	chr1:114520300..114522001-chr1:115209558..115212394,2	MCF-7	breast:
8	chr1:114519403..114521469-chr1:114543831..114545676,2	MCF-7	breast:
9	chr1:114353779..114355494-chr1:114518175..114520933,2	MCF-7	breast:
10	chr1:114519027..114521459-chr1:114540570..114543395,2	MCF-7	breast:
11	chr1:114470970..114473124-chr1:114519683..114521709,2	MCF-7	breast:
12	chr1:114519941..114520743-chr1:114888836..114889487,2	MCF-7	breast:
13	chr1:114520287..114523233-chr1:115052633..115055496,3	MCF-7	breast:
14	chr1:114520217..114521137-chr16:67188998..67189838,2	MCF-7	breast:

No data

Variant related genes	Relation type
OLFML3	TF binding region
ENSG00000081019	Chromatin interaction
ENSG00000140939	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000197323	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000270780	Chromatin interaction
ENSG00000102871	Chromatin interaction
ENSG00000179044	Chromatin interaction
ENSG00000163349	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10108	0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10494162	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs11102703	0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs11102706	0.84[ASN][1000 genomes]
rs11102707	0.89[CHD][hapmap];0.86[JPT][hapmap]
rs11102708	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11102709	0.82[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12127377	0.82[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap]
rs12129050	0.82[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap];0.84[ASN][1000 genomes]
rs1503832	0.88[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1553450	0.82[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap]
rs17852555	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1910485	0.88[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41302825	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6669370	0.88[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6674384	0.88[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs7364	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7519860	0.88[CEU][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.81[EUR][1000 genomes]
rs7545300	0.94[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7546851	0.81[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs756493	0.81[ASN][1000 genomes]
rs878129	0.88[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10494163	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs10494163	DENND2C	cis	cerebellum	SCAN
rs10494163	PTPN22	cis	parietal	SCAN
rs10494163	CD53	cis	parietal	SCAN
rs10494163	DCLRE1B	cis	lymphoblastoid	seeQTL
rs10494163	DCLRE1B	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114511200-114521800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:114512200-114521000	Weak transcription	Fetal Heart	heart
3	chr1:114512800-114521600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:114513200-114521800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:114515000-114521600	Weak transcription	Fetal Brain Male	brain
6	chr1:114516000-114521600	Weak transcription	HMEC	breast
7	chr1:114516200-114521600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:114516200-114521600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:114516200-114521600	Weak transcription	Pancreas	Pancrea
10	chr1:114516200-114521600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:114516200-114521600	Weak transcription	NHEK	skin
12	chr1:114516200-114521800	Weak transcription	Gastric	stomach
13	chr1:114516200-114522000	Weak transcription	Right Ventricle	heart
14	chr1:114516200-114524600	Weak transcription	Small Intestine	intestine
15	chr1:114516400-114521200	Weak transcription	HepG2	liver
16	chr1:114516400-114521600	Weak transcription	Aorta	Aorta
17	chr1:114517400-114521600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:114517400-114521600	Weak transcription	Colonic Mucosa	Colon
19	chr1:114517400-114521600	Enhancers	HSMMtube	muscle
20	chr1:114517400-114522400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr1:114517400-114522400	Enhancers	Primary hematopoietic stem cells	blood
22	chr1:114517600-114521200	Genic enhancers	Primary T cells from cord blood	blood
23	chr1:114517600-114521400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr1:114517600-114521400	Enhancers	Osteobl	bone
25	chr1:114517600-114521600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:114517600-114521600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:114517600-114521600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:114517600-114523400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:114517800-114521600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:114518000-114521000	Weak transcription	Fetal Intestine Small	intestine
31	chr1:114518000-114521800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:114518000-114521800	Weak transcription	Fetal Brain Female	brain
33	chr1:114518000-114524800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:114518200-114521600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:114518200-114521600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:114518200-114521600	Weak transcription	K562	blood
37	chr1:114518200-114522600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:114518400-114521400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:114518400-114521800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:114518400-114521800	Weak transcription	Hela-S3	cervix
41	chr1:114518400-114523000	Weak transcription	Thymus	Thymus
42	chr1:114518400-114525600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:114518600-114521800	Weak transcription	Brain Germinal Matrix	brain
44	chr1:114518600-114525200	Weak transcription	Dnd41	blood
45	chr1:114518800-114521200	Enhancers	NHDF-Ad	bronchial
46	chr1:114518800-114521600	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr1:114518800-114521600	Weak transcription	Fetal Intestine Large	intestine
48	chr1:114518800-114521600	Enhancers	Fetal Muscle Leg	muscle
49	chr1:114518800-114525200	Weak transcription	GM12878-XiMat	blood
50	chr1:114518800-114525800	Weak transcription	Esophagus	oesophagus

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