Variant report

Variant	rs3985801
Chromosome Location	chr15:52972380-52972381
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	FOXA1	chr15:52972278-52972577	T-47D	breast:	n/a	chr15:52972491-52972506
2	FOS	chr15:52972202-52972402	MCF10A-Er-Src	breast:	n/a	chr15:52972282-52972294 chr15:52972285-52972296 chr15:52972284-52972292 chr15:52972282-52972293
3	MAX	chr15:52970079-52972574	MCF-7	breast:	n/a	chr15:52971590-52971603 chr15:52971591-52971602 chr15:52971592-52971601 chr15:52971592-52971601 chr15:52971590-52971603 chr15:52971590-52971603 chr15:52972284-52972293
4	SIN3A	chr15:52970016-52972473	H1-hESC	embryonic stem cell:	n/a	chr15:52970877-52970890 chr15:52970919-52970932 chr15:52970845-52970856 chr15:52971384-52971395 chr15:52971685-52971698
5	RFX5	chr15:52969780-52972825	SK-N-SH	brain:	n/a	chr15:52971597-52971612 chr15:52971667-52971682 chr15:52971667-52971682 chr15:52969927-52969935 chr15:52971666-52971683 chr15:52971667-52971682
6	HCFC1	chr15:52969381-52972517	Hela-S3	cervix:	n/a	n/a
7	MAX	chr15:52972254-52972421	H1-hESC	embryonic stem cell:	n/a	chr15:52972284-52972293
8	FOXA1	chr15:52972301-52972534	T-47D	breast:	n/a	chr15:52972491-52972506
9	SIN3AK20	chr15:52969983-52972599	MCF-7	breast:	n/a	n/a
10	POLR2A	chr15:52969881-52972464	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr15:52970087-52972596	Raji	blood:	n/a	n/a
12	MAX	chr15:52972172-52972401	Hela-S3	cervix:	n/a	chr15:52972284-52972293
13	MXI1	chr15:52969974-52972602	IMR90	lung:	n/a	chr15:52971666-52971681 chr15:52971668-52971683
14	GATA3	chr15:52970173-52972684	MCF-7	breast:	n/a	chr15:52971629-52971639
15	FOS	chr15:52972271-52972416	MCF10A-Er-Src	breast:	n/a	chr15:52972282-52972294 chr15:52972285-52972296 chr15:52972284-52972292 chr15:52972282-52972293
16	JUND	chr15:52970299-52972434	MCF-7	breast:	n/a	chr15:52972282-52972294 chr15:52972285-52972296 chr15:52972284-52972292 chr15:52971115-52971127 chr15:52971116-52971126 chr15:52971708-52971722 chr15:52970749-52970758 chr15:52972282-52972293
17	FOS	chr15:52972180-52972455	MCF10A-Er-Src	breast:	n/a	chr15:52972282-52972294 chr15:52972285-52972296 chr15:52972284-52972292 chr15:52972282-52972293
18	ZNF263	chr15:52970183-52972481	HEK293-T-REx	kidney:	n/a	chr15:52971632-52971641 chr15:52970838-52970847
19	FOS	chr15:52972213-52972405	MCF10A-Er-Src	breast:	n/a	chr15:52972282-52972294 chr15:52972285-52972296 chr15:52972284-52972292 chr15:52972282-52972293
20	ELF1	chr15:52969868-52972526	MCF-7	breast:	n/a	chr15:52970870-52970883 chr15:52971641-52971653 chr15:52971350-52971362 chr15:52971263-52971275 chr15:52970922-52970934 chr15:52971785-52971794
21	MXI1	chr15:52969632-52972771	SK-N-SH	brain:	n/a	chr15:52971666-52971681 chr15:52971668-52971683
22	POLR2A	chr15:52972137-52972523	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52819791..52821534-chr15:52970285..52973265,2	MCF-7	breast:
2	chr15:52967401..52973659-chr15:53000765..53004676,11	MCF-7	breast:
3	chr15:52968259..52973250-chr15:52997483..53005703,18	MCF-7	breast:
4	chr15:52966022..52968187-chr15:52971881..52974523,2	K562	blood:
5	chr15:52855349..52864927-chr15:52966670..52972620,15	MCF-7	breast:
6	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:

Variant related genes	Relation type
FAM214A	TF binding region
ENSG00000128989	Chromatin interaction
ENSG00000047346	Chromatin interaction
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16965111	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16965128	1.00[AMR][1000 genomes]
rs2414173	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4344673	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52967400-52972400	Active TSS	Right Atrium	heart
2	chr15:52969000-52972400	Active TSS	Psoas Muscle	Psoas
3	chr15:52969000-52972400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr15:52969600-52972400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:52969600-52972400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:52969800-52972400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:52969800-52972400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:52969800-52972600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr15:52969800-52972600	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr15:52969800-52972600	Active TSS	Fetal Kidney	kidney
11	chr15:52969800-52972600	Active TSS	Right Ventricle	heart
12	chr15:52969800-52973000	Active TSS	HSMMtube	muscle
13	chr15:52970000-52972400	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr15:52970000-52972400	Active TSS	Left Ventricle	heart
15	chr15:52970000-52972600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:52970000-52972600	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr15:52970200-52972400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:52970200-52972400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:52970200-52972400	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr15:52970200-52972400	Active TSS	Colonic Mucosa	Colon
21	chr15:52970200-52972400	Active TSS	Esophagus	oesophagus
22	chr15:52970200-52972600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr15:52970200-52972600	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr15:52970400-52972400	Active TSS	Brain Hippocampus Middle	brain
25	chr15:52970400-52972400	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr15:52970400-52972600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:52970400-52972600	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr15:52970400-52972600	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr15:52970400-52972600	Active TSS	Brain Anterior Caudate	brain
30	chr15:52970400-52972600	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr15:52970600-52972400	Active TSS	H1 Cell Line	embryonic stem cell
32	chr15:52970600-52972400	Active TSS	Fetal Brain Male	brain
33	chr15:52970600-52972400	Active TSS	Fetal Muscle Trunk	muscle
34	chr15:52971200-52972400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:52971200-52972400	Active TSS	HepG2	liver
36	chr15:52971800-52972400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:52972000-52972400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:52972000-52972400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
39	chr15:52972000-52972400	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr15:52972000-52972400	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr15:52972000-52972400	Enhancers	Primary T cells fromperipheralblood	blood
42	chr15:52972000-52972400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr15:52972000-52972400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:52972000-52972400	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr15:52972000-52972400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr15:52972000-52972400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr15:52972000-52972400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr15:52972000-52972400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:52972000-52972400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:52972000-52972400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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