Variant report

Variant	rs7396866
Chromosome Location	chr11:74698928-74698929
allele	A/G
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	chr11:74698885-74701361	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:74659109..74661906-chr11:74698267..74701116,3	K562	blood:
2	chr11:74658459..74662580-chr11:74698519..74701644,8	MCF-7	breast:
3	chr11:74658436..74661013-chr11:74696774..74699429,2	MCF-7	breast:

Variant related genes	Relation type
NEU3	TF binding region
ENSG00000166435	Chromatin interaction
ENSG00000118363	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10751241	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs10793107	0.95[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10793108	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899051	0.84[AMR][1000 genomes]
rs10899052	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs10899053	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899054	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899058	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10899059	0.88[ASN][1000 genomes]
rs10899060	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11236281	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11236282	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11236289	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11236290	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11236294	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236296	0.87[ASN][1000 genomes]
rs11603294	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12221841	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs12225372	0.82[AMR][1000 genomes]
rs12225387	0.81[AMR][1000 genomes]
rs12419113	0.82[AMR][1000 genomes]
rs12419929	0.82[AMR][1000 genomes]
rs12575200	0.82[AMR][1000 genomes]
rs12577127	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12577614	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1371410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17133461	0.92[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs2119028	0.96[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2165162	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2165163	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2298746	0.92[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs2304683	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs3814726	0.86[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap]
rs4245440	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4387374	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4456280	0.90[GIH][hapmap]
rs4483614	0.92[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs4944960	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs4944961	0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap]
rs4944965	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944968	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56194145	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59143825	0.82[AMR][1000 genomes]
rs59328242	0.83[AMR][1000 genomes]
rs61671395	0.82[AMR][1000 genomes]
rs61894779	0.80[AMR][1000 genomes]
rs61894839	0.82[AMR][1000 genomes]
rs7102619	0.83[AMR][1000 genomes]
rs7105085	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs7128739	0.92[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs725460	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7483351	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs919877	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes]
rs9787775	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9787897	0.84[AMR][1000 genomes];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	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:27)

SNP	Gene	Cis/trans	Tissue	Source
rs7396866	XRRA1	cis	cerebellum	SCAN
rs7396866	RNF169	cis	lymphoblastoid	seeQTL
rs7396866	XRRA1	cis	Heart Left Ventricle	GTEx
rs7396866	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs7396866	XRRA1	cis	Whole Blood	GTEx
rs7396866	XRRA1	cis	parietal	SCAN
rs7396866	XRRA1	cis	Muscle Skeletal	GTEx
rs7396866	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs7396866	XRRA1	cis	Esophagus Mucosa	GTEx
rs7396866	XRRA1	cis	Esophagus Muscularis	GTEx
rs7396866	XRRA1	cis	Artery Tibial	GTEx
rs7396866	RNF169	cis	cerebellum	SCAN
rs7396866	XRRA1	cis	lymphoblastoid	GTEx
rs7396866	PAAF1	cis	parietal	SCAN
rs7396866	XRRA1	cis	Artery Aorta	GTEx
rs7396866	XRRA1	cis	normal skin	skin_eQTL
rs7396866	RP11-147I3.1	cis	Thyroid	GTEx
rs7396866	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs7396866	XRRA1	cis	Adipose Subcutaneous	GTEx
rs7396866	XRRA1	cis	lesional skin	skin_eQTL
rs7396866	XRRA1	cis	lymphoblastoid	seeQTL
rs7396866	PLEKHB1	cis	cerebellum	SCAN
rs7396866	XRRA1	cis	Stomach	GTEx
rs7396866	XRRA1	cis	lung	GTEx
rs7396866	XRRA1	cis	Thyroid	GTEx
rs7396866	XRRA1	cis	Nerve Tibial	GTEx
rs7396866	RN7SL239P	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74661800-74699200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:74661800-74699400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:74662200-74699600	Weak transcription	Esophagus	oesophagus
4	chr11:74675600-74699400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:74678600-74699200	Weak transcription	Spleen	Spleen
6	chr11:74681000-74699200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:74681200-74699600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:74684400-74699200	Weak transcription	Pancreas	Pancrea
9	chr11:74684800-74699200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:74686400-74699400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:74686800-74699200	Weak transcription	Aorta	Aorta
12	chr11:74686800-74699400	Weak transcription	Fetal Brain Male	brain
13	chr11:74687200-74699200	Weak transcription	Right Ventricle	heart
14	chr11:74687600-74699600	Weak transcription	NHEK	skin
15	chr11:74687800-74699600	Weak transcription	Colon Smooth Muscle	Colon
16	chr11:74687800-74700000	Weak transcription	Fetal Heart	heart
17	chr11:74689400-74699200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:74689400-74699200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:74689400-74699200	Weak transcription	Hela-S3	cervix
20	chr11:74689400-74699200	Weak transcription	HUVEC	blood vessel
21	chr11:74689400-74699400	Weak transcription	Brain Anterior Caudate	brain
22	chr11:74689400-74699400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr11:74689400-74699600	Weak transcription	Brain Hippocampus Middle	brain
24	chr11:74689600-74699000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:74689600-74699200	Weak transcription	Primary B cells from cord blood	blood
26	chr11:74689600-74699200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr11:74689600-74699200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr11:74689600-74699200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr11:74689600-74699200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr11:74689600-74699200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr11:74689600-74699400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:74689600-74699400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr11:74689600-74699400	Weak transcription	NHLF	lung
34	chr11:74689600-74699600	Weak transcription	Brain Substantia Nigra	brain
35	chr11:74689800-74699200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr11:74689800-74699200	Weak transcription	Colonic Mucosa	Colon
37	chr11:74690000-74699000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr11:74690000-74699200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr11:74690000-74699400	Weak transcription	NHDF-Ad	bronchial
40	chr11:74690200-74699200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr11:74690200-74699200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr11:74690200-74699200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:74690200-74699200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr11:74690200-74699600	Weak transcription	Small Intestine	intestine
45	chr11:74690400-74699200	Weak transcription	Brain Angular Gyrus	brain
46	chr11:74690600-74699400	Weak transcription	Ovary	ovary
47	chr11:74691000-74699200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr11:74691000-74699200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr11:74691200-74699200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:74691200-74699200	Weak transcription	A549	lung

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