Variant report

Variant	rs60389828
Chromosome Location	chr15:38857631-38857632
allele	C/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	chr15:38856783-38857685	H1-hESC	embryonic stem cell:	n/a	chr15:38856887-38856897
2	MYC	chr15:38857538-38857651	MCF-7	breast:	n/a	n/a
3	POLR2A	chr15:38855773-38857651	Raji	blood:	n/a	n/a
4	BHLHE40	chr15:38856863-38857635	GM12878	blood:	n/a	chr15:38857344-38857360 chr15:38856900-38856916
5	E2F6	chr15:38856720-38857758	H1-hESC	embryonic stem cell:	n/a	chr15:38857340-38857347 chr15:38857012-38857021 chr15:38857340-38857347 chr15:38857340-38857347
6	MTA3	chr15:38856866-38857659	GM12878	blood:	n/a	n/a
7	MAX	chr15:38856751-38857755	H1-hESC	embryonic stem cell:	n/a	chr15:38856887-38856897
8	RAD21	chr15:38856000-38857721	SK-N-SH	brain:	n/a	chr15:38856388-38856402 chr15:38856000-38856014 chr15:38857635-38857649 chr15:38856386-38856400 chr15:38856388-38856397 chr15:38856392-38856404 chr15:38856387-38856406
9	E2F6	chr15:38856841-38857751	H1-hESC	embryonic stem cell:	n/a	chr15:38857340-38857347 chr15:38857012-38857021 chr15:38857340-38857347 chr15:38857340-38857347
10	CTBP2	chr15:38855868-38857758	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:38744991..38746966-chr15:38854872..38857693,2	MCF-7	breast:
2	chr15:38834085..38836050-chr15:38857165..38859463,2	MCF-7	breast:
3	chr15:38855702..38858314-chr15:38985984..38988881,2	MCF-7	breast:

Variant related genes	Relation type
RASGRP1	TF binding region
ENSG00000171262	Chromatin interaction
ENSG00000201509	Chromatin interaction
ENSG00000175779	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11636932	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16967035	0.88[ASN][1000 genomes]
rs35843594	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4923800	0.83[EUR][1000 genomes]
rs4924274	0.85[EUR][1000 genomes]
rs55699464	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56170975	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56231408	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62006162	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62006164	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62006165	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62008298	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949171	chr15:38232548-39033746	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv904085	chr15:38786114-38985513	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv525770	chr15:38816833-39084956	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1054651	chr15:38827825-39082844	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv542358	chr15:38827825-39082844	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv904086	chr15:38829198-38931396	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	esv3415080	chr15:38855685-38858233	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38855000-38857800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr15:38855600-38857800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr15:38856000-38857800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr15:38856000-38857800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr15:38856000-38857800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr15:38856200-38857800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
7	chr15:38856200-38857800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr15:38856200-38857800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr15:38856200-38857800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr15:38856400-38857800	Active TSS	Brain Cingulate Gyrus	brain
11	chr15:38857000-38857800	Bivalent Enhancer	Fetal Brain Male	brain
12	chr15:38857200-38857800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:38857200-38857800	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr15:38857200-38857800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr15:38857200-38857800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:38857200-38857800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr15:38857200-38857800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:38857200-38857800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr15:38857200-38857800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr15:38857200-38857800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr15:38857200-38857800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
22	chr15:38857200-38857800	Enhancers	Spleen	Spleen
23	chr15:38857200-38858000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr15:38857200-38858400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr15:38857400-38857800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:38857400-38857800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:38857400-38857800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:38857400-38857800	Bivalent Enhancer	Placenta	Placenta
29	chr15:38857400-38857800	Enhancers	Gastric	stomach
30	chr15:38857400-38857800	Bivalent Enhancer	Stomach Mucosa	stomach
31	chr15:38857400-38858000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr15:38857600-38857800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:38857600-38857800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:38857600-38857800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:38857600-38857800	Enhancers	Primary B cells from cord blood	blood
36	chr15:38857600-38857800	Enhancers	Primary B cells from peripheral blood	blood
37	chr15:38857600-38857800	Enhancers	Primary hematopoietic stem cells	blood
38	chr15:38857600-38857800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
39	chr15:38857600-38857800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:38857600-38857800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:38857600-38857800	Enhancers	Esophagus	oesophagus
42	chr15:38857600-38857800	Bivalent Enhancer	Fetal Intestine Large	intestine
43	chr15:38857600-38857800	Bivalent Enhancer	Fetal Intestine Small	intestine
44	chr15:38857600-38857800	Enhancers	Pancreas	Pancrea
45	chr15:38857600-38857800	Enhancers	Dnd41	blood
46	chr15:38857600-38857800	Enhancers	GM12878-XiMat	blood
47	chr15:38857600-38858000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:38857600-38858000	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr15:38857600-38858000	Enhancers	Thymus	Thymus
50	chr15:38857600-38859200	Enhancers	Fetal Thymus	thymus

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