Variant report

Variant	rs7162885
Chromosome Location	chr15:52403854-52403855
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	CTCF	chr15:52403720-52403870	GM12864	blood:	n/a	chr15:52403764-52403774
2	POLR2A	chr15:52403812-52404027	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:52403762-52405802	NB4	blood:	n/a	n/a
4	POLR2A	chr15:52403715-52405006	GM19193	blood:	n/a	n/a
5	POLR2A	chr15:52403564-52404976	GM12891	blood:	n/a	n/a
6	MTA3	chr15:52403416-52404901	GM12878	blood:	n/a	n/a
7	RUNX3	chr15:52403564-52403990	GM12878	blood:	n/a	n/a
8	CTCF	chr15:52403820-52403970	NB4	blood:	n/a	n/a
9	ELF1	chr15:52403663-52404665	GM12878	blood:	n/a	n/a
10	YY1	chr15:52403803-52404283	GM12891	blood:	n/a	chr15:52404061-52404071
11	CTCF	chr15:52403720-52403870	GM12875	blood:	n/a	chr15:52403764-52403774
12	PML	chr15:52403631-52404813	GM12878	blood:	n/a	n/a
13	CTCF	chr15:52403771-52403944	GM12878	blood:	n/a	n/a
14	WRNIP1	chr15:52403829-52403985	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:52403681-52404911	GM12891	blood:	n/a	n/a
16	POLR2A	chr15:52403797-52404959	GM12891	blood:	n/a	n/a
17	RUNX3	chr15:52403563-52404049	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52388531..52391551-chr15:52401411..52403881,3	MCF-7	breast:
2	chr15:52393212..52395889-chr15:52402587..52404691,2	K562	blood:

Variant related genes	Relation type
ENSG00000259327	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16953085	0.82[AFR][1000 genomes]
rs16964737	0.82[AFR][1000 genomes]
rs2231296	0.86[AFR][1000 genomes]
rs7163133	0.82[AFR][1000 genomes]
rs7164357	0.82[AFR][1000 genomes]
rs73402839	0.96[AFR][1000 genomes]
rs73402853	0.82[AFR][1000 genomes]
rs73402859	0.82[AFR][1000 genomes]
rs73402869	0.82[AFR][1000 genomes]
rs8024767	0.82[AFR][1000 genomes]
rs8035146	0.81[AFR][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:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52398600-52404200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr15:52399000-52404000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:52399400-52404000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:52401000-52404200	Enhancers	Primary B cells from peripheral blood	blood
5	chr15:52402200-52404200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:52402200-52404200	Weak transcription	Pancreas	Pancrea
7	chr15:52402200-52411400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:52402400-52405600	Weak transcription	HepG2	liver
9	chr15:52402800-52404000	Weak transcription	Spleen	Spleen
10	chr15:52403600-52404000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:52403600-52404200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr15:52403600-52404200	Weak transcription	HMEC	breast
13	chr15:52403600-52404800	Flanking Active TSS	GM12878-XiMat	blood
14	chr15:52403800-52404000	Enhancers	Colonic Mucosa	Colon
15	chr15:52403800-52404200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr15:52403800-52404200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr15:52403800-52404200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:52403800-52404200	Bivalent Enhancer	Fetal Brain Female	brain
19	chr15:52403800-52404400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:52403800-52404400	Bivalent Enhancer	Fetal Intestine Small	intestine

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