Variant report

Variant	rs997465
Chromosome Location	chr11:74699193-74699194
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr11:74699167-74699804	K562	blood:	n/a	n/a
2	EGR1	chr11:74699193-74699446	K562	blood:	n/a	n/a
3	POLR2A	chr11:74698965-74700880	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:74699158-74700599	GM12892	blood:	n/a	n/a
5	MTA3	chr11:74699192-74700773	GM12878	blood:	n/a	n/a
6	CEBPB	chr11:74699186-74699399	K562	blood:	n/a	n/a
7	RCOR1	chr11:74699135-74700410	K562	blood:	n/a	n/a
8	POLR2A	chr11:74699186-74700583	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr11:74699137-74700517	PANC-1	pancreas:	n/a	n/a
10	MXI1	chr11:74698994-74700921	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr11:74698885-74701361	GM12891	blood:	n/a	n/a
12	EGR1	chr11:74699163-74699424	K562	blood:	n/a	n/a
13	PML	chr11:74699135-74700411	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:74699014-74700405	K562	blood:	n/a	n/a
15	POLR2A	chr11:74699168-74700397	GM12892	blood:	n/a	n/a

No data

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

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:

No data

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

Extended variants
information (count: 65 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10899066	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs11236269	0.81[AMR][1000 genomes]
rs11605604	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs12363224	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1282460	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1282461	0.81[AMR][1000 genomes]
rs1282689	0.84[ASN][1000 genomes]
rs1282690	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1282692	0.86[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs1282695	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1292895	0.86[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs1297319	0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1583342	0.93[ASW][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.96[MKK][hapmap]
rs2028343	0.86[ASN][1000 genomes]
rs2028344	0.86[ASN][1000 genomes]
rs2033532	0.80[ASW][hapmap];0.87[JPT][hapmap]
rs2851136	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2919057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4245439	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4373962	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4592443	0.84[AFR][1000 genomes]
rs471462	0.93[ASW][hapmap];0.94[JPT][hapmap];0.92[MKK][hapmap]
rs473256	0.80[ASW][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs480840	0.93[ASW][hapmap];0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap]
rs488115	0.85[MEX][hapmap]
rs4944067	0.82[MKK][hapmap];0.84[TSI][hapmap]
rs508319	0.81[AMR][1000 genomes]
rs511021	0.86[ASN][1000 genomes]
rs511890	0.86[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs512780	0.93[ASW][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap]
rs513137	0.93[JPT][hapmap]
rs519741	0.93[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.92[MKK][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs527529	0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs529249	0.81[AMR][1000 genomes]
rs529488	0.80[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs537054	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs538502	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs543244	0.93[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.92[MKK][hapmap];0.84[ASN][1000 genomes]
rs546643	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs550491	1.00[CHB][hapmap]
rs550869	0.86[ASN][1000 genomes]
rs550980	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs561589	0.94[JPT][hapmap]
rs562265	0.84[ASN][1000 genomes]
rs567956	0.93[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.96[MKK][hapmap];0.84[ASN][1000 genomes]
rs568558	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs568758	0.83[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs577063	0.90[ASN][1000 genomes]
rs590105	0.86[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs594144	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs599722	0.93[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.92[MKK][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs603062	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs614832	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs616085	0.84[ASN][1000 genomes]
rs624786	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs625268	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs629573	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs641584	0.86[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs643807	0.93[ASW][hapmap];0.80[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs646287	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs688665	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs7121374	0.83[YRI][hapmap]
rs7938876	0.87[ASN][1000 genomes]
rs9444	0.85[ASW][hapmap];0.87[JPT][hapmap];0.85[MKK][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	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs997465	KRTAP5-10	cis	parietal	SCAN
rs997465	XRRA1	cis	parietal	SCAN
rs997465	XRRA1	cis	Whole Blood	GTEx
rs997465	RNF169	cis	cerebellum	SCAN
rs997465	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs997465	XRRA1	cis	cerebellum	SCAN
rs997465	RNF169	cis	lymphoblastoid	seeQTL
rs997465	XRRA1	cis	lymphoblastoid	seeQTL
rs997465	PLEKHB1	cis	cerebellum	SCAN

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	chr11:74689600-74699200	Weak transcription	Primary B cells from cord blood	blood
25	chr11:74689600-74699200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:74689600-74699200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr11:74689600-74699200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr11:74689600-74699200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr11:74689600-74699200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:74689600-74699400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:74689600-74699400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:74689600-74699400	Weak transcription	NHLF	lung
33	chr11:74689600-74699600	Weak transcription	Brain Substantia Nigra	brain
34	chr11:74689800-74699200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr11:74689800-74699200	Weak transcription	Colonic Mucosa	Colon
36	chr11:74690000-74699200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr11:74690000-74699400	Weak transcription	NHDF-Ad	bronchial
38	chr11:74690200-74699200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr11:74690200-74699200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:74690200-74699200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:74690200-74699200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:74690200-74699600	Weak transcription	Small Intestine	intestine
43	chr11:74690400-74699200	Weak transcription	Brain Angular Gyrus	brain
44	chr11:74690600-74699400	Weak transcription	Ovary	ovary
45	chr11:74691000-74699200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:74691000-74699200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr11:74691200-74699200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr11:74691200-74699200	Weak transcription	A549	lung
49	chr11:74691200-74699200	Weak transcription	Osteobl	bone
50	chr11:74691400-74699200	Weak transcription	Primary T cells fromperipheralblood	blood

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