Variant report

Variant	rs1149602
Chromosome Location	chr11:76479810-76479811
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	MAX	chr11:76479498-76480509	NB4	blood:	n/a	n/a
2	RCOR1	chr11:76479589-76480037	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:76478822-76481511	A549	lung:	n/a	n/a
4	EP300	chr11:76479176-76484206	A549	lung:	n/a	chr11:76482306-76482319 chr11:76480952-76480961 chr11:76483592-76483602 chr11:76481902-76481916
5	MXI1	chr11:76479565-76480063	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:76479293-76479896	A549	lung:	n/a	n/a
7	POLR2A	chr11:76479519-76480011	HL-60	blood:	n/a	n/a
8	MAZ	chr11:76479537-76479935	Hela-S3	cervix:	n/a	n/a
9	TBP	chr11:76479528-76480006	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr11:76478856-76481555	A549	lung:	n/a	n/a
11	JUND	chr11:76479107-76479844	A549	lung:	n/a	n/a
12	POLR2A	chr11:76479529-76479947	Hela-S3	cervix:	n/a	n/a
13	SMARCB1	chr11:76478986-76481405	Hela-S3	cervix:	n/a	chr11:76480951-76480960
14	STAT3	chr11:76479627-76479948	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr11:76479532-76479946	ECC-1	luminal epithelium:	n/a	n/a
16	GATA3	chr11:76479526-76482690	A549	lung:	n/a	chr11:76480629-76480646
17	ZKSCAN1	chr11:76479590-76479991	Hela-S3	cervix:	n/a	n/a
18	ELK1	chr11:76479753-76480140	Hela-S3	cervix:	n/a	n/a
19	MAFK	chr11:76479654-76479931	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr11:76479535-76480083	HL-60	blood:	n/a	n/a
21	EP300	chr11:76479629-76479955	Hela-S3	cervix:	n/a	n/a
22	MYC	chr11:76479495-76480360	NB4	blood:	n/a	n/a
23	CEBPB	chr11:76479549-76480256	Hela-S3	cervix:	n/a	n/a
24	SIX5	chr11:76479461-76482870	A549	lung:	n/a	n/a
25	USF2	chr11:76479623-76479940	Hela-S3	cervix:	n/a	n/a
26	BCL3	chr11:76479486-76482939	A549	lung:	n/a	chr11:76480327-76480336 chr11:76480952-76480961 chr11:76481907-76481916
27	RAD21	chr11:76479550-76480022	Hela-S3	cervix:	n/a	n/a
28	REST	chr11:76479484-76482566	A549	lung:	n/a	chr11:76482046-76482059
29	MAX	chr11:76479743-76483468	A549	lung:	n/a	chr11:76480952-76480961
30	TCF12	chr11:76479802-76482463	A549	lung:	n/a	chr11:76482146-76482153 chr11:76480716-76480726 chr11:76482255-76482265 chr11:76480990-76480997
31	POLR2A	chr11:76479514-76481125	A549	lung:	n/a	n/a
32	SP1	chr11:76479170-76480097	A549	lung:	n/a	chr11:76480073-76480087
33	GTF2F1	chr11:76479191-76479946	Hela-S3	cervix:	n/a	n/a
34	SPI1	chr11:76479504-76480017	HL-60	blood:	n/a	chr11:76479775-76479788
35	MAX	chr11:76478401-76484386	A549	lung:	n/a	chr11:76480952-76480961
36	ETS1	chr11:76479665-76481591	A549	lung:	n/a	chr11:76480074-76480088 chr11:76480224-76480237
37	POLR2A	chr11:76479158-76482608	HepG2	liver:	n/a	n/a
38	REST	chr11:76479536-76479984	A549	lung:	n/a	n/a
39	EP300	chr11:76479517-76484254	A549	lung:	n/a	chr11:76482306-76482319 chr11:76480952-76480961 chr11:76483592-76483602 chr11:76481902-76481916
40	POLR2A	chr11:76478778-76481454	A549	lung:	n/a	n/a
41	FOXA1	chr11:76479647-76480045	HepG2	liver:	n/a	n/a
42	ZNF143	chr11:76479646-76479946	Hela-S3	cervix:	n/a	n/a
43	FOSL2	chr11:76479564-76482987	A549	lung:	n/a	chr11:76480951-76480961 chr11:76480952-76480960 chr11:76480949-76480960 chr11:76480951-76480961 chr11:76480952-76480959 chr11:76480951-76480961 chr11:76480950-76480962 chr11:76480952-76480960 chr11:76480951-76480961
44	CHD2	chr11:76479336-76479838	Hela-S3	cervix:	n/a	n/a
45	TCF12	chr11:76477960-76484560	A549	lung:	n/a	chr11:76482146-76482153 chr11:76480716-76480726 chr11:76482255-76482265 chr11:76480990-76480997 chr11:76483592-76483601
46	RFX5	chr11:76479663-76479914	Hela-S3	cervix:	n/a	n/a
47	PBX3	chr11:76479038-76481305	A549	lung:	n/a	n/a
48	SMC3	chr11:76479153-76479927	Hela-S3	cervix:	n/a	n/a
49	SP1	chr11:76478891-76484193	A549	lung:	n/a	chr11:76480073-76480087 chr11:76482603-76482612 chr11:76480707-76480719 chr11:76481685-76481695 chr11:76482249-76482263 chr11:76480708-76480717 chr11:76480709-76480718 chr11:76481685-76481695 chr11:76480707-76480719 chr11:76480859-76480873
50	MAX	chr11:76479534-76482534	Hela-S3	cervix:	n/a	chr11:76480952-76480961

No.	Distal block	Cell Line	Cell type
1	chr11:76479684..76482260-chr11:85435259..85436958,2	MCF-7	breast:
2	chr11:76478547..76482353-chr11:76570414..76574348,5	MCF-7	breast:
3	chr11:76479171..76486141-chr11:76745972..76752965,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254632	TF binding region
ENSG00000078124	Chromatin interaction
ENSG00000137501	Chromatin interaction
ENSG00000198488	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1149595	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1149600	0.99[EUR][1000 genomes]
rs1149603	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1149611	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.80[MEX][hapmap];0.82[ASN][1000 genomes]
rs1149613	0.84[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1224953	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1224954	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs876361	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1149602	P2RY6	cis	parietal	SCAN
rs1149602	RP11-21L23.4	cis	Adipose Subcutaneous	GTEx
rs1149602	WNT11	cis	parietal	SCAN
rs1149602	GUCY2EP	cis	Thyroid	GTEx
rs1149602	GUCY2EP	cis	Adipose Subcutaneous	GTEx
rs1149602	RP11-672A2.1	cis	Adipose Subcutaneous	GTEx
rs1149602	SNORD15B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76470600-76482000	Weak transcription	Psoas Muscle	Psoas
2	chr11:76473600-76483200	Enhancers	Esophagus	oesophagus
3	chr11:76474000-76481000	Enhancers	Fetal Muscle Trunk	muscle
4	chr11:76474000-76481200	Enhancers	Spleen	Spleen
5	chr11:76474000-76485600	Enhancers	Left Ventricle	heart
6	chr11:76474400-76485400	Enhancers	Fetal Muscle Leg	muscle
7	chr11:76475000-76480800	Enhancers	Fetal Brain Male	brain
8	chr11:76475400-76481800	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:76476200-76485600	Enhancers	Fetal Intestine Large	intestine
10	chr11:76476400-76484400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr11:76476400-76485200	Enhancers	Fetal Intestine Small	intestine
12	chr11:76477200-76480000	Transcr. at gene 5' and 3'	A549	lung
13	chr11:76477400-76484000	Weak transcription	Aorta	Aorta
14	chr11:76477600-76480600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:76477800-76480200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr11:76478000-76480800	Flanking Active TSS	Liver	Liver
17	chr11:76478000-76481200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:76478200-76480000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:76478200-76480400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:76478200-76481000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:76478400-76480200	Enhancers	Primary T cells from cord blood	blood
22	chr11:76478400-76480200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:76478400-76480200	Enhancers	Stomach Mucosa	stomach
24	chr11:76478400-76480800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr11:76478400-76481000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:76478400-76481000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr11:76478400-76481200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr11:76478400-76482200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr11:76478400-76483000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr11:76478400-76483200	Enhancers	HMEC	breast
31	chr11:76478400-76485400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr11:76478600-76480000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:76478600-76480000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr11:76478600-76480200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr11:76478600-76480200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr11:76478600-76480200	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr11:76478600-76480200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr11:76478600-76480400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr11:76478600-76480600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:76478600-76480800	Enhancers	Fetal Lung	lung
41	chr11:76478600-76480800	Enhancers	Ovary	ovary
42	chr11:76478600-76481200	Enhancers	Right Ventricle	heart
43	chr11:76478600-76482800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:76478600-76483200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:76478600-76483600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:76478600-76483600	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr11:76478600-76483600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:76478600-76483800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr11:76478800-76480000	Enhancers	Brain Angular Gyrus	brain
50	chr11:76478800-76480000	Enhancers	Brain Germinal Matrix	brain

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