Variant report

Variant	rs1800849
Chromosome Location	chr11:73720165-73720166
allele	C/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	chr11:73720047-73720293	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
UCP3	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10431176	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs10501415	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs10898955	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs10898957	0.84[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs10898960	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs10898961	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10898962	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs10898963	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs11235965	0.87[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11235971	1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11235972	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11235988	0.82[ASN][1000 genomes]
rs11235994	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap]
rs11235995	0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap]
rs11235996	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs11235998	0.85[AFR][1000 genomes]
rs11235999	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs11236000	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap]
rs11236003	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11236027	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11236029	0.95[CHB][hapmap];0.92[CHD][hapmap]
rs11600314	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs11602451	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs11604125	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11604713	0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs11606804	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11607335	0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11608147	0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs12223320	0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap]
rs12574038	0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap]
rs12574039	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs12574047	0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap]
rs12574556	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs12575211	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1527302	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs1565125	0.82[EUR][1000 genomes]
rs1615607	0.82[ASN][1000 genomes]
rs1685333	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17132715	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1800006	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2075576	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2178000	0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs3741135	1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs3814724	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs4019299	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4539349	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4565925	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs59900762	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7110734	0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs7115407	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs7125032	0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap]
rs7930460	1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs826035	0.82[ASN][1000 genomes]
rs826044	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]

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	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1800849	PPME1	cis	cerebellum	SCAN
rs1800849	PGM2L1	cis	multi-tissue	Pritchard
rs1800849	STARD10	cis	parietal	SCAN
rs1800849	FOLR3	cis	parietal	SCAN
rs1800849	UCP2	cis	multi-tissue	Pritchard
rs1800849	P4HA3	cis	cerebellum	SCAN
rs1800849	ANO1	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73708800-73729400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:73709000-73724200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:73710200-73728400	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:73710600-73741800	Weak transcription	Fetal Kidney	kidney
5	chr11:73710600-73748800	Weak transcription	Fetal Brain Male	brain
6	chr11:73710800-73722400	Weak transcription	NHDF-Ad	bronchial
7	chr11:73711000-73721200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr11:73711000-73729200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr11:73711800-73720200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:73711800-73729200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:73712000-73721200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:73712200-73721200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:73712200-73726800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:73712200-73743600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr11:73712200-73743800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:73712400-73721800	Weak transcription	Colonic Mucosa	Colon
17	chr11:73712600-73722400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:73712800-73743400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr11:73713600-73725000	Weak transcription	A549	lung
20	chr11:73714000-73726000	Weak transcription	Esophagus	oesophagus
21	chr11:73714200-73729800	Weak transcription	Hela-S3	cervix
22	chr11:73714600-73727200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr11:73714800-73721400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:73714800-73721600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr11:73714800-73724000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:73715000-73722200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr11:73715000-73729800	Weak transcription	Ovary	ovary
28	chr11:73715200-73721000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:73715200-73722000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:73715200-73722600	Weak transcription	NHLF	lung
31	chr11:73715200-73722800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:73715200-73727200	Weak transcription	Fetal Lung	lung
33	chr11:73715200-73727400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:73715400-73720400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr11:73715400-73721400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr11:73715400-73722600	Weak transcription	HSMMtube	muscle
37	chr11:73715400-73727400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:73715600-73721200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:73715600-73722000	Weak transcription	HSMM	muscle
40	chr11:73716000-73723400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr11:73716200-73721000	Weak transcription	Brain Anterior Caudate	brain
42	chr11:73716200-73722400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:73716200-73722600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:73716200-73722800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:73716200-73723400	Weak transcription	Gastric	stomach
46	chr11:73716200-73727600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:73716400-73721000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr11:73716400-73721200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr11:73716400-73722200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr11:73716400-73723600	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links