Variant report

Variant	rs11870781
Chromosome Location	chr17:45383295-45383296
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	POLR2A	chr17:45382744-45383366	SK-N-SH	brain:	n/a	n/a
2	JUN	chr17:45382736-45383309	HUVEC	blood vessel:	n/a	chr17:45383017-45383027 chr17:45383017-45383027 chr17:45383017-45383027
3	FOXA1	chr17:45382830-45383396	HepG2	liver:	n/a	chr17:45383116-45383131
4	GATA3	chr17:45382369-45383595	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr17:45382567-45383570	A549	lung:	n/a	chr17:45382834-45382841
6	FOXA1	chr17:45382870-45383316	HepG2	liver:	n/a	chr17:45383116-45383131
7	TEAD4	chr17:45382731-45383484	A549	lung:	n/a	n/a
8	EP300	chr17:45382761-45383372	A549	lung:	n/a	n/a
9	EP300	chr17:45382626-45383554	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr17:45382681-45383377	MCF-7	breast:	n/a	n/a
11	SIN3AK20	chr17:45382696-45383512	MCF-7	breast:	n/a	n/a
12	JUND	chr17:45382652-45383468	SK-N-SH	brain:	n/a	chr17:45383017-45383027 chr17:45383017-45383027 chr17:45383017-45383027
13	RCOR1	chr17:45382706-45383343	Hela-S3	cervix:	n/a	n/a
14	TEAD4	chr17:45382575-45383441	ECC-1	luminal epithelium:	n/a	n/a
15	STAT3	chr17:45382358-45383295	MCF10A-Er-Src	breast:	n/a	chr17:45382582-45382590 chr17:45382796-45382803 chr17:45382924-45382936
16	FOXM1	chr17:45382432-45383579	ECC-1	luminal epithelium:	n/a	n/a
17	FOXA1	chr17:45382790-45383335	ECC-1	luminal epithelium:	n/a	chr17:45383116-45383131
18	EP300	chr17:45382732-45383506	A549	lung:	n/a	n/a
19	EP300	chr17:45382589-45383446	ECC-1	luminal epithelium:	n/a	n/a
20	CEBPB	chr17:45382767-45383391	Hela-S3	cervix:	n/a	n/a
21	TEAD4	chr17:45382656-45383550	SK-N-SH	brain:	n/a	n/a
22	HDAC2	chr17:45382713-45383385	MCF-7	breast:	n/a	n/a
23	NFIC	chr17:45382397-45383623	SK-N-SH	brain:	n/a	n/a
24	RFX5	chr17:45382823-45383327	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr17:45382442-45383490	HUVEC	blood vessel:	n/a	n/a
26	SP1	chr17:45382685-45383472	A549	lung:	n/a	n/a
27	TCF12	chr17:45382541-45383451	ECC-1	luminal epithelium:	n/a	chr17:45382834-45382841
28	FOXA1	chr17:45382894-45383310	ECC-1	luminal epithelium:	n/a	chr17:45383116-45383131
29	GATA3	chr17:45382638-45383494	A549	lung:	n/a	n/a
30	EP300	chr17:45382595-45383565	SK-N-SH	brain:	n/a	n/a
31	TCF12	chr17:45382283-45383608	ECC-1	luminal epithelium:	n/a	chr17:45382290-45382299 chr17:45382834-45382841
32	BRCA1	chr17:45382888-45383349	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr17:45382700-45383380	HUVEC	blood vessel:	n/a	n/a
34	FOXA2	chr17:45382832-45383427	A549	lung:	n/a	n/a
35	MYC	chr17:45382627-45383302	MCF10A-Er-Src	breast:	n/a	n/a
36	GATA3	chr17:45382415-45383498	SK-N-SH	brain:	n/a	n/a
37	ESR1	chr17:45382744-45383302	ECC-1	luminal epithelium:	n/a	n/a
38	FOXA2	chr17:45382675-45383351	A549	lung:	n/a	n/a
39	FOSL2	chr17:45382861-45383363	SK-N-SH	brain:	n/a	chr17:45383017-45383027 chr17:45383017-45383027 chr17:45383017-45383027
40	STAT3	chr17:45382451-45383299	MCF10A-Er-Src	breast:	n/a	chr17:45382582-45382590 chr17:45382796-45382803 chr17:45382924-45382936
41	PBX3	chr17:45382493-45383409	SK-N-SH	brain:	n/a	n/a
42	FOSL2	chr17:45382688-45383312	A549	lung:	n/a	chr17:45383017-45383027 chr17:45383017-45383027 chr17:45383017-45383027
43	FOS	chr17:45382565-45383379	MCF10A-Er-Src	breast:	n/a	chr17:45383016-45383027 chr17:45383017-45383027 chr17:45383017-45383027 chr17:45383017-45383027
44	STAT3	chr17:45382299-45383539	MCF10A-Er-Src	breast:	n/a	chr17:45382582-45382590 chr17:45382796-45382803 chr17:45382924-45382936
45	CEBPB	chr17:45382566-45383343	ECC-1	luminal epithelium:	n/a	n/a
46	FOS	chr17:45382552-45383330	MCF10A-Er-Src	breast:	n/a	chr17:45383016-45383027 chr17:45383017-45383027 chr17:45383017-45383027 chr17:45383017-45383027
47	NR2F2	chr17:45382642-45383451	MCF-7	breast:	n/a	n/a
48	GATA3	chr17:45382559-45383330	T-47D	breast:	n/a	n/a
49	GATA3	chr17:45382642-45383371	MCF-7	breast:	n/a	n/a
50	FOXA1	chr17:45382690-45383425	T-47D	breast:	n/a	chr17:45383116-45383131

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45382065..45383991-chr17:45399117..45400961,2	K562	blood:

Variant related genes	Relation type
ENSG00000263293	TF binding region
ENSG00000178852	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11079765	0.86[JPT][hapmap]
rs11079771	0.85[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs11867192	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11867253	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11867589	0.84[JPT][hapmap]
rs11868344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868912	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11869768	0.84[JPT][hapmap]
rs11869835	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11871031	0.84[JPT][hapmap]
rs11871477	0.84[JPT][hapmap]
rs12051664	0.84[JPT][hapmap]
rs12051702	0.84[JPT][hapmap]
rs12162128	0.98[ASN][1000 genomes]
rs13306485	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16941751	0.86[JPT][hapmap]
rs16941771	0.84[JPT][hapmap]
rs16941855	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941861	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878067	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2292700	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2317676	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785870	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs3785873	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41304764	0.88[ASN][1000 genomes]
rs55706706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56722403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5919	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73322309	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8073229	0.95[AMR][1000 genomes];0.84[EUR][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	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11870781	C17orf57	Cis_1M	lymphoblastoid	RTeQTL
rs11870781	EFCAB13	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45357200-45398000	Weak transcription	Psoas Muscle	Psoas
2	chr17:45359000-45389800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr17:45371400-45393000	Weak transcription	Dnd41	blood
4	chr17:45372400-45383600	Weak transcription	Gastric	stomach
5	chr17:45372400-45389600	Weak transcription	Esophagus	oesophagus
6	chr17:45372400-45389800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr17:45372400-45394400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr17:45374000-45392800	Weak transcription	Brain Substantia Nigra	brain
9	chr17:45375400-45388400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr17:45376200-45389200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr17:45377200-45383400	Weak transcription	Pancreas	Pancrea
12	chr17:45379600-45390400	Weak transcription	Fetal Intestine Small	intestine
13	chr17:45380200-45392800	Weak transcription	Brain Hippocampus Middle	brain
14	chr17:45380400-45387800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr17:45381200-45383800	Enhancers	NHDF-Ad	bronchial
16	chr17:45381400-45383800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:45381400-45392600	Weak transcription	Liver	Liver
18	chr17:45381600-45383800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr17:45381600-45384000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr17:45381600-45384400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr17:45381800-45384600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr17:45381800-45387400	Weak transcription	Placenta	Placenta
23	chr17:45381800-45387600	Weak transcription	Fetal Intestine Large	intestine
24	chr17:45381800-45392800	Weak transcription	Left Ventricle	heart
25	chr17:45382200-45383800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr17:45382200-45384000	Enhancers	NHLF	lung
27	chr17:45382200-45385000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr17:45382200-45385200	Enhancers	Hela-S3	cervix
29	chr17:45382400-45383600	Enhancers	Rectal Smooth Muscle	rectum
30	chr17:45382400-45383600	Enhancers	GM12878-XiMat	blood
31	chr17:45382400-45383800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr17:45382400-45383800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr17:45382400-45383800	Enhancers	Stomach Mucosa	stomach
34	chr17:45382400-45383800	Enhancers	HSMM	muscle
35	chr17:45382400-45383800	Enhancers	HSMMtube	muscle
36	chr17:45382400-45383800	Enhancers	Osteobl	bone
37	chr17:45382400-45384000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr17:45382400-45384000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr17:45382400-45384000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr17:45382400-45385000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr17:45382400-45385000	Enhancers	HMEC	breast
42	chr17:45382600-45383400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr17:45382600-45383400	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr17:45382600-45383400	Flanking Active TSS	NH-A	brain
45	chr17:45382600-45383600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr17:45382600-45383600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr17:45382600-45383600	Enhancers	Adipose Nuclei	Adipose
48	chr17:45382600-45383600	Enhancers	Colon Smooth Muscle	Colon
49	chr17:45382600-45383800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr17:45382600-45383800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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