Variant report

Variant	rs11164905
Chromosome Location	chr1:93790294-93790295
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	MAX	chr1:93790178-93790833	Hela-S3	cervix:	n/a	chr1:93790563-93790572
2	EP300	chr1:93789977-93790953	Hela-S3	cervix:	n/a	chr1:93790562-93790571 chr1:93790563-93790572
3	RCOR1	chr1:93790144-93790897	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:93790229-93790901	MCF10A-Er-Src	breast:	n/a	n/a
5	FOSL2	chr1:93790064-93790866	A549	lung:	n/a	chr1:93790563-93790572 chr1:93790563-93790571 chr1:93790564-93790571 chr1:93790562-93790571
6	STAT3	chr1:93790232-93790803	MCF10A-Er-Src	breast:	n/a	chr1:93790563-93790572 chr1:93790562-93790571
7	CEBPB	chr1:93790078-93790936	Hela-S3	cervix:	n/a	n/a
8	FOS	chr1:93790126-93790867	MCF10A-Er-Src	breast:	n/a	chr1:93790563-93790572 chr1:93790563-93790571 chr1:93790561-93790572 chr1:93790564-93790571 chr1:93790562-93790571
9	FOXA1	chr1:93790177-93790333	T-47D	breast:	n/a	n/a
10	STAT3	chr1:93790270-93790791	MCF10A-Er-Src	breast:	n/a	chr1:93790563-93790572 chr1:93790562-93790571
11	CEBPB	chr1:93790095-93790493	MCF-7	breast:	n/a	n/a
12	MYC	chr1:93790229-93790796	MCF10A-Er-Src	breast:	n/a	chr1:93790563-93790572
13	MAX	chr1:93790252-93790804	Hela-S3	cervix:	n/a	chr1:93790563-93790572
14	FOS	chr1:93790234-93790979	MCF10A-Er-Src	breast:	n/a	chr1:93790563-93790572 chr1:93790563-93790571 chr1:93790561-93790572 chr1:93790564-93790571 chr1:93790562-93790571
15	SMC3	chr1:93790216-93791032	Hela-S3	cervix:	n/a	n/a
16	USF2	chr1:93790256-93790756	Hela-S3	cervix:	n/a	n/a
17	MYC	chr1:93790177-93790869	Hela-S3	cervix:	n/a	chr1:93790563-93790572
18	MXI1	chr1:93790289-93790883	Hela-S3	cervix:	n/a	n/a
19	JUND	chr1:93790106-93790916	Hela-S3	cervix:	n/a	chr1:93790563-93790572 chr1:93790563-93790571 chr1:93790564-93790571 chr1:93790561-93790572 chr1:93790562-93790571
20	CEBPB	chr1:93790155-93790429	H1-hESC	embryonic stem cell:	n/a	n/a
21	RAD21	chr1:93790181-93790876	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr1:93790130-93790421	K562	blood:	n/a	n/a
23	GATA3	chr1:93790129-93790340	T-47D	breast:	n/a	n/a
24	CEBPB	chr1:93790121-93790498	A549	lung:	n/a	n/a
25	NFIC	chr1:93790291-93790829	ECC-1	luminal epithelium:	n/a	n/a
26	TBP	chr1:93789994-93790871	Hela-S3	cervix:	n/a	n/a
27	FOXA2	chr1:93790008-93790748	A549	lung:	n/a	chr1:93790548-93790560
28	FOS	chr1:93790126-93790984	MCF10A-Er-Src	breast:	n/a	chr1:93790563-93790572 chr1:93790563-93790571 chr1:93790561-93790572 chr1:93790564-93790571 chr1:93790562-93790571
29	SP1	chr1:93789964-93790777	A549	lung:	n/a	n/a
30	GATA3	chr1:93790112-93790392	T-47D	breast:	n/a	n/a
31	CEBPB	chr1:93790059-93790514	A549	lung:	n/a	n/a
32	JUN	chr1:93790044-93790961	Hela-S3	cervix:	n/a	chr1:93790563-93790572 chr1:93790563-93790571 chr1:93790564-93790571 chr1:93790562-93790571
33	GATA3	chr1:93789887-93790940	A549	lung:	n/a	n/a
34	STAT3	chr1:93790224-93790960	Hela-S3	cervix:	n/a	chr1:93790563-93790572 chr1:93790562-93790571
35	MYC	chr1:93790235-93790981	MCF10A-Er-Src	breast:	n/a	chr1:93790563-93790572
36	TCF12	chr1:93789943-93790648	A549	lung:	n/a	n/a
37	NR3C1	chr1:93790108-93790317	A549	lung:	n/a	n/a
38	SP1	chr1:93790077-93790798	A549	lung:	n/a	n/a
39	CEBPB	chr1:93790114-93790683	A549	lung:	n/a	n/a
40	CHD2	chr1:93790158-93790781	Hela-S3	cervix:	n/a	n/a
41	GATA3	chr1:93790135-93790554	MCF-7	breast:	n/a	n/a
42	BRCA1	chr1:93789600-93790947	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr1:93790268-93790765	Hela-S3	cervix:	n/a	n/a
44	CEBPB	chr1:93790111-93790842	IMR90	lung:	n/a	n/a
45	SRF	chr1:93790243-93790833	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr1:93790290-93790645	Hela-S3	cervix:	n/a	n/a
47	RFX5	chr1:93790097-93790974	Hela-S3	cervix:	n/a	n/a
48	FOS	chr1:93790113-93790809	Hela-S3	cervix:	n/a	chr1:93790563-93790572 chr1:93790563-93790571 chr1:93790561-93790572 chr1:93790564-93790571 chr1:93790562-93790571

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93789215..93790995-chr1:93809839..93812682,2	K562	blood:
2	chr1:93788744..93790531-chr1:93809891..93812646,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223745	TF binding region
ENSG00000117505	Chromatin interaction
ENSG00000223745	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10874766	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11164896	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164897	0.83[ASN][1000 genomes]
rs11164908	0.89[ASN][1000 genomes]
rs12027142	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12031709	0.86[ASN][1000 genomes]
rs12033147	0.82[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036057	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038046	0.88[EUR][1000 genomes]
rs12045001	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12046063	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12048219	0.80[ASN][1000 genomes]
rs12405487	0.86[ASN][1000 genomes]
rs12563120	0.87[ASN][1000 genomes]
rs12563709	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12566752	0.89[ASN][1000 genomes]
rs2255722	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs2391251	0.86[ASN][1000 genomes]
rs2484486	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs2783490	0.81[CEU][hapmap]
rs2783493	0.82[EUR][1000 genomes]
rs2783495	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs2783496	0.84[EUR][1000 genomes]
rs2783497	0.86[EUR][1000 genomes]
rs2783505	0.88[EUR][1000 genomes]
rs28782525	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2893242	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3087457	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35628716	0.82[ASN][1000 genomes]
rs35910103	0.81[ASN][1000 genomes]
rs35915989	0.80[ASN][1000 genomes]
rs3904666	0.81[CEU][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4847425	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61266405	0.89[ASN][1000 genomes]
rs61799470	0.88[EUR][1000 genomes]
rs61799497	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61799516	0.86[ASN][1000 genomes]
rs61799517	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61799538	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676902	0.86[ASN][1000 genomes]
rs6684908	0.86[ASN][1000 genomes]
rs698927	0.82[ASN][1000 genomes]
rs771454	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs771458	0.82[ASN][1000 genomes]
rs771461	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs771462	0.82[ASN][1000 genomes]
rs771465	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs771470	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs771476	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs771479	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs771482	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs810027	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11164905	DR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93751600-93794600	Weak transcription	Brain Substantia Nigra	brain
2	chr1:93753000-93803600	Weak transcription	Adipose Nuclei	Adipose
3	chr1:93753200-93806400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:93755400-93802600	Weak transcription	Primary B cells from cord blood	blood
5	chr1:93755400-93803200	Weak transcription	Fetal Thymus	thymus
6	chr1:93755600-93803400	Weak transcription	Fetal Intestine Large	intestine
7	chr1:93755600-93804200	Weak transcription	Brain Anterior Caudate	brain
8	chr1:93755800-93801400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:93756000-93803800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr1:93765800-93809800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:93767800-93801400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:93768600-93791600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:93768600-93803000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:93772600-93806000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:93779600-93804000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:93783000-93803400	Weak transcription	Left Ventricle	heart
17	chr1:93783800-93801200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:93784400-93804000	Weak transcription	Thymus	Thymus
19	chr1:93786200-93803800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:93786400-93791800	Enhancers	Stomach Mucosa	stomach
21	chr1:93787400-93790400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:93788600-93790400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:93789000-93797200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:93789000-93803800	Weak transcription	Placenta	Placenta
25	chr1:93789200-93790400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:93789200-93810200	Weak transcription	Esophagus	oesophagus
27	chr1:93789400-93790600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr1:93789400-93791200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:93789400-93793400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:93789600-93790600	Enhancers	HMEC	breast
31	chr1:93789600-93800400	Weak transcription	Primary T cells from cord blood	blood
32	chr1:93789600-93806600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr1:93789800-93790400	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr1:93789800-93791000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr1:93789800-93791400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:93789800-93791400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:93790000-93790400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:93790000-93790600	Enhancers	Duodenum Mucosa	Duodenum
39	chr1:93790000-93790600	Flanking Active TSS	HSMMtube	muscle
40	chr1:93790000-93791000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr1:93790200-93790400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:93790200-93790400	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr1:93790200-93790400	Enhancers	Osteobl	bone
44	chr1:93790200-93790600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:93790200-93790600	Enhancers	Liver	Liver
46	chr1:93790200-93790600	Active TSS	Hela-S3	cervix
47	chr1:93790200-93790600	Enhancers	HUVEC	blood vessel
48	chr1:93790200-93790600	Enhancers	NH-A	brain
49	chr1:93790200-93790800	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr1:93790200-93790800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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