Variant report

Variant	rs1292895
Chromosome Location	chr11:74664025-74664026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr11:74663640-74664396	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr11:74663723-74664383	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr11:74663821-74664046	ProgFib	skin:	n/a	n/a
4	REST	chr11:74663536-74664554	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr11:74663734-74664268	H1-neurons	neurons:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:74658556..74662613-chr11:74662682..74668168,9	MCF-7	breast:
2	chr11:74662206..74664890-chr11:74672995..74675273,3	K562	blood:
3	chr11:74663493..74665057-chr11:74721622..74724251,2	K562	blood:
4	chr11:74662428..74664987-chr11:74667630..74670235,3	K562	blood:
5	chr11:74631321..74634356-chr11:74663906..74665643,3	K562	blood:

No data

Variant related genes	Relation type
XRRA1	TF binding region
ENSG00000118363	Chromatin interaction
ENSG00000166435	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11236269	0.94[ASN][1000 genomes]
rs11605604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12363224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1282460	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1282461	0.83[ASN][1000 genomes]
rs1282689	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1282690	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1282692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1282695	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1297319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1315297	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1583342	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2028343	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2028344	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033532	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2851136	0.83[ASN][1000 genomes]
rs2919057	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs41531051	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4245439	0.84[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap]
rs471462	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs473080	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs473256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs480840	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[ASN][1000 genomes]
rs495246	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs502225	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs505688	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs508319	0.92[ASN][1000 genomes]
rs511021	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511890	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs512780	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap]
rs513137	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs519741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527529	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs529249	0.94[ASN][1000 genomes]
rs529488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537054	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs538502	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs543244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546643	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550491	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550869	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550980	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs557483	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs561589	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs562265	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs568758	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs571446	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs573925	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577063	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577102	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs580142	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs590105	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs603062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616085	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs625268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs629573	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643807	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs688665	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs997465	0.86[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.84[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	nsv832210	chr11:74562782-74732133	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs1292895	RNF169	cis	cerebellum	SCAN
rs1292895	XRRA1	cis	lung	GTEx
rs1292895	XRRA1	cis	Whole Blood	GTEx
rs1292895	XRRA1	cis	Esophagus Mucosa	GTEx
rs1292895	RP11-147I3.1	cis	Thyroid	GTEx
rs1292895	XRRA1	cis	lymphoblastoid	seeQTL
rs1292895	XRRA1	cis	parietal	SCAN
rs1292895	KRTAP5-10	cis	parietal	SCAN
rs1292895	RNF169	cis	lymphoblastoid	seeQTL
rs1292895	XRRA1	cis	Thyroid	GTEx
rs1292895	XRRA1	cis	Adipose Subcutaneous	GTEx
rs1292895	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs1292895	XRRA1	cis	Artery Tibial	GTEx
rs1292895	XRRA1	cis	Muscle Skeletal	GTEx
rs1292895	XRRA1	cis	cerebellum	SCAN
rs1292895	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74661200-74665400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:74661200-74688600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:74661600-74686000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:74661800-74672600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr11:74661800-74675000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:74661800-74699200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:74661800-74699400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:74662000-74664800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:74662000-74664800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:74662000-74665200	Weak transcription	Placenta	Placenta
11	chr11:74662000-74665200	Weak transcription	Right Atrium	heart
12	chr11:74662000-74665400	Weak transcription	Ovary	ovary
13	chr11:74662000-74669800	Weak transcription	Fetal Intestine Small	intestine
14	chr11:74662000-74677600	Weak transcription	HSMMtube	muscle
15	chr11:74662000-74680800	Weak transcription	Fetal Kidney	kidney
16	chr11:74662000-74682200	Weak transcription	Aorta	Aorta
17	chr11:74662000-74682800	Weak transcription	Colonic Mucosa	Colon
18	chr11:74662200-74664600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr11:74662200-74665200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr11:74662200-74665600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:74662200-74665800	Weak transcription	Osteobl	bone
22	chr11:74662200-74666400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr11:74662200-74666600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:74662200-74667000	Weak transcription	Brain Substantia Nigra	brain
25	chr11:74662200-74667000	Weak transcription	Psoas Muscle	Psoas
26	chr11:74662200-74667000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:74662200-74671000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:74662200-74671600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:74662200-74672800	Weak transcription	Gastric	stomach
30	chr11:74662200-74672800	Weak transcription	Stomach Mucosa	stomach
31	chr11:74662200-74677000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr11:74662200-74677200	Weak transcription	Fetal Muscle Leg	muscle
33	chr11:74662200-74677200	Weak transcription	Thymus	Thymus
34	chr11:74662200-74677800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:74662200-74677800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:74662200-74699600	Weak transcription	Esophagus	oesophagus
37	chr11:74662400-74664200	Enhancers	Fetal Heart	heart
38	chr11:74662400-74664400	Weak transcription	Pancreas	Pancrea
39	chr11:74662400-74664800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr11:74662400-74665000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr11:74662400-74665400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr11:74662400-74666000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:74662400-74666600	Strong transcription	A549	lung
44	chr11:74662400-74667000	Weak transcription	Right Ventricle	heart
45	chr11:74662400-74667200	Weak transcription	Brain Hippocampus Middle	brain
46	chr11:74662400-74667400	Weak transcription	Brain Anterior Caudate	brain
47	chr11:74662400-74667600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr11:74662400-74668400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr11:74662400-74668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr11:74662400-74668600	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links