Variant report

Variant	rs2289074
Chromosome Location	chr11:9636376-9636377
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:32)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:32 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:9481140..9484022-chr11:9635844..9638076,2	MCF-7	breast:
2	chr11:9622499..9625012-chr11:9634792..9636736,2	K562	blood:
3	chr11:9634797..9636840-chr11:9770227..9772919,2	MCF-7	breast:
4	chr11:9625140..9628957-chr11:9633939..9638776,5	K562	blood:
5	chr11:9634944..9638366-chr11:9672187..9674812,3	K562	blood:
6	chr11:9635234..9636871-chr11:9761636..9763417,2	MCF-7	breast:
7	chr11:9634746..9636757-chr11:9685229..9688142,2	MCF-7	breast:
8	chr11:9605204..9607351-chr11:9635673..9637421,2	K562	blood:
9	chr11:9634831..9638731-chr11:9777356..9781938,7	K562	blood:
10	chr11:9479842..9485152-chr11:9633556..9639403,13	K562	blood:
11	chr11:9594264..9596863-chr11:9633913..9636459,6	K562	blood:
12	chr11:9634288..9636670-chr11:9753675..9757139,3	MCF-7	breast:
13	chr11:9597111..9603831-chr11:9632388..9638176,11	K562	blood:
14	chr11:9633888..9637224-chr11:9645529..9649937,4	K562	blood:
15	chr11:9634299..9636932-chr11:9637562..9639803,2	MCF-7	breast:
16	chr11:9586513..9589428-chr11:9634913..9638092,4	K562	blood:
17	chr11:9593146..9594870-chr11:9635191..9636726,2	MCF-7	breast:
18	chr11:9634112..9636653-chr11:9679644..9682405,2	K562	blood:
19	chr11:9635704..9636420-chr11:9769574..9770431,2	MCF-7	breast:
20	chr11:9587790..9592116-chr11:9635065..9637852,3	MCF-7	breast:
21	chr11:9593380..9601954-chr11:9626466..9639393,32	K562	blood:
22	chr11:9634859..9637342-chr11:9650481..9653341,3	K562	blood:
23	chr11:9554823..9558413-chr11:9633918..9637025,5	K562	blood:
24	chr11:9634169..9637157-chr11:9770583..9773571,2	MCF-7	breast:
25	chr11:9384438..9386089-chr11:9633922..9636673,2	MCF-7	breast:
26	chr11:9604448..9606704-chr11:9634785..9637173,2	K562	blood:
27	chr11:9633888..9638474-chr11:9645827..9648910,5	K562	blood:
28	chr11:9635657..9637159-chr11:9686246..9687885,2	MCF-7	breast:
29	chr11:9479781..9484865-chr11:9633607..9638660,10	K562	blood:
30	chr11:9629347..9631467-chr11:9634646..9636480,2	MCF-7	breast:
31	chr11:9586141..9589428-chr11:9634451..9638092,8	K562	blood:
32	chr11:9586720..9588950-chr11:9633664..9636381,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000166478	Chromatin interaction
ENSG00000246273	Chromatin interaction
ENSG00000245522	Chromatin interaction
ENSG00000239470	Chromatin interaction
ENSG00000243964	Chromatin interaction
ENSG00000268403	Chromatin interaction
ENSG00000243869	Chromatin interaction
ENSG00000255463	Chromatin interaction
ENSG00000238387	Chromatin interaction
ENSG00000133789	Chromatin interaction
ENSG00000166483	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10770043	0.87[JPT][hapmap]
rs10770047	0.87[JPT][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs10840269	0.82[TSI][hapmap]
rs10840270	0.87[CEU][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10840271	0.82[ASN][1000 genomes]
rs10840274	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12273601	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.96[ASN][1000 genomes]
rs12419525	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12420438	0.83[CEU][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2060477	0.94[ASN][1000 genomes]
rs4910059	0.83[CEU][hapmap]
rs57701122	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7109545	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7109585	0.94[ASN][1000 genomes]
rs7118466	0.94[ASN][1000 genomes]
rs7118581	0.94[ASN][1000 genomes]
rs7124238	0.93[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	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2289074	OR52E6	cis	parietal	SCAN
rs2289074	SWAP70	cis	lymphoblastoid	seeQTL
rs2289074	SWAP70	cis	cerebellum	SCAN
rs2289074	HPX	cis	cerebellum	SCAN
rs2289074	SWAP70	cis	multi-tissue	Pritchard
rs2289074	SWAP70	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9634200-9636400	Flanking Active TSS	Dnd41	blood
2	chr11:9634400-9636600	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr11:9634400-9636600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr11:9634400-9636800	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr11:9634400-9636800	Enhancers	Fetal Heart	heart
6	chr11:9634400-9636800	Flanking Active TSS	HUVEC	blood vessel
7	chr11:9634400-9637000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:9634600-9636400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr11:9634600-9636400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr11:9634600-9636400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr11:9634600-9636400	Active TSS	Brain Angular Gyrus	brain
12	chr11:9634600-9636400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr11:9634600-9636400	Active TSS	Thymus	Thymus
14	chr11:9634600-9636600	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr11:9634600-9637000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:9634600-9637200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr11:9634800-9636400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr11:9634800-9636400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:9634800-9636400	Active TSS	Brain Anterior Caudate	brain
20	chr11:9634800-9636400	Flanking Active TSS	Fetal Muscle Trunk	muscle
21	chr11:9634800-9636400	Flanking Active TSS	NHEK	skin
22	chr11:9634800-9636600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:9635000-9636400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr11:9635000-9636400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr11:9635000-9636400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:9635000-9636400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:9635000-9636400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr11:9635000-9636400	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr11:9635000-9636400	Flanking Active TSS	Fetal Stomach	stomach
30	chr11:9635000-9636400	Active TSS	Right Atrium	heart
31	chr11:9635000-9636400	Flanking Active TSS	NH-A	brain
32	chr11:9635000-9636600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr11:9635000-9637000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr11:9635400-9636800	Weak transcription	Spleen	Spleen
35	chr11:9635400-9646400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:9635600-9636400	Active TSS	K562	blood
37	chr11:9635800-9636400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:9635800-9636400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr11:9635800-9636400	Flanking Active TSS	Stomach Mucosa	stomach
40	chr11:9635800-9636600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:9635800-9637000	Flanking Active TSS	Hela-S3	cervix
42	chr11:9636000-9636400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
43	chr11:9636000-9636400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:9636000-9636400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:9636000-9636400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr11:9636000-9636400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:9636000-9636400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:9636000-9636400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr11:9636000-9636400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr11:9636000-9636400	Flanking Active TSS	Brain Hippocampus Middle	brain

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