Variant report

Variant	rs7171700
Chromosome Location	chr15:52392829-52392830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:82)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:82 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL11A	chr15:52392661-52393036	GM12878	blood:	n/a	n/a
2	IRF4	chr15:52392536-52393336	GM12878	blood:	n/a	n/a
3	TCF3	chr15:52392786-52393042	GM12878	blood:	n/a	n/a
4	EP300	chr15:52392637-52393256	GM12878	blood:	n/a	n/a
5	TAF1	chr15:52392780-52393038	GM12892	blood:	n/a	n/a
6	IRF4	chr15:52392459-52393199	GM12878	blood:	n/a	n/a
7	BCL11A	chr15:52392660-52393367	GM12878	blood:	n/a	n/a
8	SP1	chr15:52392663-52393332	GM12878	blood:	n/a	n/a
9	BHLHE40	chr15:52392639-52393211	HepG2	liver:	n/a	n/a
10	TCF12	chr15:52392636-52393290	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:52392821-52392908	K562	blood:	n/a	n/a
12	FOS	chr15:52392632-52393394	MCF10A-Er-Src	breast:	n/a	chr15:52393208-52393219 chr15:52393233-52393244
13	MXI1	chr15:52392682-52392970	HepG2	liver:	n/a	n/a
14	CHD2	chr15:52392484-52393310	GM12878	blood:	n/a	n/a
15	BATF	chr15:52392717-52393418	GM12878	blood:	n/a	n/a
16	RELA	chr15:52392559-52393318	GM18951	blood:	n/a	n/a
17	MXI1	chr15:52392472-52393409	IMR90	lung:	n/a	n/a
18	PAX5	chr15:52392620-52393299	GM12878	blood:	n/a	n/a
19	ATF2	chr15:52392403-52392931	GM12878	blood:	n/a	n/a
20	USF2	chr15:52392597-52392857	GM12878	blood:	n/a	n/a
21	TCF7L2	chr15:52392578-52393315	Hela-S3	cervix:	n/a	n/a
22	EBF1	chr15:52392504-52393423	GM12878	blood:	n/a	n/a
23	NFIC	chr15:52392504-52393491	GM12878	blood:	n/a	n/a
24	SP1	chr15:52392636-52393344	GM12878	blood:	n/a	n/a
25	POLR2A	chr15:52392550-52393322	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:52392619-52393384	GM12878	blood:	n/a	n/a
27	BHLHE40	chr15:52392402-52393433	GM12878	blood:	n/a	n/a
28	MYC	chr15:52392624-52393312	MCF10A-Er-Src	breast:	n/a	n/a
29	EBF1	chr15:52392646-52393454	GM12878	blood:	n/a	n/a
30	MXI1	chr15:52392519-52393371	GM12878	blood:	n/a	n/a
31	MAZ	chr15:52392457-52393181	GM12878	blood:	n/a	n/a
32	RELA	chr15:52392524-52393310	GM19099	blood:	n/a	n/a
33	CHD1	chr15:52392517-52393292	GM12878	blood:	n/a	n/a
34	POU2F2	chr15:52392422-52393367	GM12878	blood:	n/a	n/a
35	MXI1	chr15:52392689-52393330	Hela-S3	cervix:	n/a	n/a
36	WRNIP1	chr15:52392435-52393041	GM12878	blood:	n/a	n/a
37	MAX	chr15:52392496-52393446	A549	lung:	n/a	n/a
38	POLR2A	chr15:52392412-52393337	GM12892	blood:	n/a	n/a
39	JUND	chr15:52392529-52393821	SK-N-SH	brain:	n/a	chr15:52393233-52393244 chr15:52393208-52393219
40	ZNF143	chr15:52392542-52393282	GM12878	blood:	n/a	n/a
41	PAX5	chr15:52392659-52393320	GM12878	blood:	n/a	n/a
42	MYC	chr15:52392664-52392859	MCF10A-Er-Src	breast:	n/a	n/a
43	MAX	chr15:52392697-52392896	K562	blood:	n/a	n/a
44	POLR2A	chr15:52392628-52393110	GM12892	blood:	n/a	n/a
45	MAX	chr15:52392628-52393345	NB4	blood:	n/a	n/a
46	RUNX3	chr15:52392334-52393373	GM12878	blood:	n/a	n/a
47	MAX	chr15:52392448-52393427	GM12878	blood:	n/a	n/a
48	RUNX3	chr15:52392371-52393450	GM12878	blood:	n/a	n/a
49	POLR2A	chr15:52392457-52393370	GM12892	blood:	n/a	n/a
50	NFIC	chr15:52392587-52393402	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:52385731..52388322-chr15:52391743..52394058,2	MCF-7	breast:
2	chr15:52309194..52314432-chr15:52385325..52393461,10	MCF-7	breast:
3	chr15:52361939..52363808-chr15:52392804..52395653,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259712	TF binding region
ENSG00000242327	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10400852	1.00[EUR][1000 genomes]
rs16953085	1.00[EUR][1000 genomes]
rs16964735	1.00[EUR][1000 genomes]
rs16964737	1.00[EUR][1000 genomes]
rs16964750	1.00[EUR][1000 genomes]
rs16964770	1.00[EUR][1000 genomes]
rs2231296	1.00[EUR][1000 genomes]
rs28656256	1.00[EUR][1000 genomes]
rs28663157	1.00[EUR][1000 genomes]
rs41494446	1.00[EUR][1000 genomes]
rs59195841	1.00[EUR][1000 genomes]
rs59289747	1.00[EUR][1000 genomes]
rs60397096	1.00[EUR][1000 genomes]
rs7163133	1.00[EUR][1000 genomes]
rs7164357	1.00[EUR][1000 genomes]
rs7165157	1.00[EUR][1000 genomes]
rs7165527	1.00[EUR][1000 genomes]
rs7165708	1.00[EUR][1000 genomes]
rs7167133	1.00[EUR][1000 genomes]
rs7172939	1.00[EUR][1000 genomes]
rs7178038	1.00[EUR][1000 genomes]
rs730945	1.00[EUR][1000 genomes]
rs73402803	1.00[EUR][1000 genomes]
rs73402824	1.00[EUR][1000 genomes]
rs73402826	1.00[EUR][1000 genomes]
rs73402833	1.00[EUR][1000 genomes]
rs73402839	1.00[EUR][1000 genomes]
rs73402853	1.00[EUR][1000 genomes]
rs73402859	1.00[EUR][1000 genomes]
rs73402869	1.00[EUR][1000 genomes]
rs73402879	1.00[EUR][1000 genomes]
rs73404813	1.00[EUR][1000 genomes]
rs8023921	1.00[EUR][1000 genomes]
rs8024311	1.00[EUR][1000 genomes]
rs8024767	1.00[EUR][1000 genomes]
rs8035146	1.00[EUR][1000 genomes]
rs8040458	1.00[EUR][1000 genomes]
rs8041042	1.00[EUR][1000 genomes]
rs8041128	1.00[EUR][1000 genomes]
rs8041233	1.00[EUR][1000 genomes]
rs8041355	1.00[EUR][1000 genomes]
rs8041504	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52385800-52395400	Weak transcription	Fetal Kidney	kidney
2	chr15:52386200-52399000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:52386600-52393000	Weak transcription	Right Atrium	heart
4	chr15:52387600-52395200	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:52387600-52395400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:52387600-52395400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:52387600-52396600	Weak transcription	Spleen	Spleen
8	chr15:52387600-52396800	Weak transcription	Esophagus	oesophagus
9	chr15:52387800-52393000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:52387800-52393000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:52387800-52393000	Weak transcription	Small Intestine	intestine
12	chr15:52387800-52393000	Weak transcription	HSMMtube	muscle
13	chr15:52388000-52393200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:52389600-52393000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:52389800-52393000	Weak transcription	HSMM	muscle
16	chr15:52391000-52393000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:52391800-52393200	Flanking Active TSS	Hela-S3	cervix
18	chr15:52391800-52397000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:52391800-52397000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr15:52392200-52395400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:52392200-52400800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:52392400-52393200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr15:52392400-52393400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:52392400-52393400	Flanking Active TSS	GM12878-XiMat	blood
25	chr15:52392400-52393600	Enhancers	NHLF	lung
26	chr15:52392400-52394200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:52392400-52394800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr15:52392400-52394800	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr15:52392400-52396800	Enhancers	A549	lung
30	chr15:52392400-52397000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:52392400-52397000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:52392400-52397000	Enhancers	NHDF-Ad	bronchial
33	chr15:52392400-52398600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:52392600-52393200	Enhancers	Ovary	ovary
35	chr15:52392600-52393200	Flanking Active TSS	HepG2	liver
36	chr15:52392600-52393400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:52392600-52393400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:52392600-52393400	Enhancers	Fetal Thymus	thymus
39	chr15:52392600-52393400	Enhancers	Osteobl	bone
40	chr15:52392600-52393600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:52392600-52393600	Enhancers	Fetal Muscle Leg	muscle
42	chr15:52392600-52393600	Enhancers	K562	blood
43	chr15:52392600-52393800	Enhancers	NH-A	brain
44	chr15:52392600-52394000	Enhancers	Fetal Muscle Trunk	muscle
45	chr15:52392600-52394600	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr15:52392600-52396200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr15:52392600-52398600	Enhancers	HMEC	breast
48	chr15:52392600-52398600	Enhancers	NHEK	skin
49	chr15:52392800-52393000	Enhancers	Placenta	Placenta
50	chr15:52392800-52393000	Enhancers	Sigmoid Colon	Sigmoid Colon

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