Variant report

Variant	rs574650946
Chromosome Location	chr15:38857353-38857354
allele	A/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	HA-E2F1	chr15:38856691-38857418	MCF-7	breast:	n/a	chr15:38857340-38857347 chr15:38857012-38857021 chr15:38857340-38857347 chr15:38857340-38857347
2	MAX	chr15:38856783-38857685	H1-hESC	embryonic stem cell:	n/a	chr15:38856887-38856897
3	POLR2A	chr15:38852140-38857375	GM12878	blood:	n/a	n/a
4	CTCF	chr15:38857260-38857410	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr15:38856259-38857623	MCF-7	breast:	n/a	n/a
6	CTCF	chr15:38855490-38857435	SK-N-SH	brain:	n/a	chr15:38856420-38856428 chr15:38856386-38856404 chr15:38856391-38856401 chr15:38856386-38856399 chr15:38856903-38856916 chr15:38856389-38856402 chr15:38856389-38856402 chr15:38856388-38856409 chr15:38856389-38856398 chr15:38856387-38856403 chr15:38856379-38856392
7	CTCF	chr15:38857240-38857390	AG04449	skin:	n/a	n/a
8	POLR2A	chr15:38855773-38857651	Raji	blood:	n/a	n/a
9	YY1	chr15:38856679-38857357	GM12878	blood:	n/a	chr15:38856690-38856699 chr15:38856902-38856916 chr15:38856886-38856895 chr15:38856901-38856910 chr15:38856898-38856909 chr15:38856830-38856844
10	MTA3	chr15:38856966-38857443	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:38855775-38857469	GM15510	blood:	n/a	n/a
12	BHLHE40	chr15:38856863-38857635	GM12878	blood:	n/a	chr15:38857344-38857360 chr15:38856900-38856916
13	CHD1	chr15:38854483-38857484	GM12878	blood:	n/a	chr15:38857153-38857163
14	E2F6	chr15:38856874-38857362	A549	lung:	n/a	chr15:38857340-38857347 chr15:38857012-38857021 chr15:38857340-38857347 chr15:38857340-38857347
15	POLR2A	chr15:38855485-38857360	GM12892	blood:	n/a	n/a
16	JUND	chr15:38857103-38857398	H1-hESC	embryonic stem cell:	n/a	n/a
17	E2F6	chr15:38856720-38857758	H1-hESC	embryonic stem cell:	n/a	chr15:38857340-38857347 chr15:38857012-38857021 chr15:38857340-38857347 chr15:38857340-38857347
18	EBF1	chr15:38856677-38857524	GM12878	blood:	n/a	chr15:38857211-38857224 chr15:38857325-38857334 chr15:38857213-38857223 chr15:38857323-38857336 chr15:38857212-38857223
19	MTA3	chr15:38856866-38857659	GM12878	blood:	n/a	n/a
20	MAX	chr15:38856751-38857755	H1-hESC	embryonic stem cell:	n/a	chr15:38856887-38856897
21	BACH1	chr15:38856848-38857462	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr15:38856698-38857355	ECC-1	luminal epithelium:	n/a	chr15:38856887-38856897
23	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
24	MAX	chr15:38856735-38857364	MCF-7	breast:	n/a	chr15:38856887-38856897
25	ELF1	chr15:38855861-38857516	GM12878	blood:	n/a	chr15:38856506-38856518 chr15:38856901-38856910 chr15:38856611-38856623 chr15:38856373-38856385 chr15:38857143-38857155 chr15:38857376-38857388
26	POLR2A	chr15:38854455-38857370	GM19099	blood:	n/a	n/a
27	CHD2	chr15:38855886-38857474	GM12878	blood:	n/a	chr15:38857153-38857163
28	MAX	chr15:38856740-38857398	MCF-7	breast:	n/a	chr15:38856887-38856897
29	POLR2A	chr15:38855602-38857412	GM18951	blood:	n/a	n/a
30	HDAC2	chr15:38856908-38857394	MCF-7	breast:	n/a	chr15:38857029-38857038
31	POLR2A	chr15:38855272-38857408	GM19193	blood:	n/a	n/a
32	PML	chr15:38856807-38857376	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:38855692-38857399	GM12892	blood:	n/a	n/a
34	E2F6	chr15:38856841-38857751	H1-hESC	embryonic stem cell:	n/a	chr15:38857340-38857347 chr15:38857012-38857021 chr15:38857340-38857347 chr15:38857340-38857347
35	HMGN3	chr15:38856260-38857421	K562	blood:	n/a	n/a
36	ZEB1	chr15:38856816-38857358	GM12878	blood:	n/a	chr15:38857267-38857278
37	MAX	chr15:38856721-38857367	A549	lung:	n/a	chr15:38856887-38856897
38	RCOR1	chr15:38855906-38857401	GM12878	blood:	n/a	n/a
39	CTBP2	chr15:38855868-38857758	H1-hESC	embryonic stem cell:	n/a	n/a
40	RUNX3	chr15:38856788-38857361	GM12878	blood:	n/a	n/a
41	EBF1	chr15:38856924-38857509	GM12878	blood:	n/a	chr15:38857211-38857224 chr15:38857325-38857334 chr15:38857213-38857223 chr15:38857323-38857336 chr15:38857212-38857223
42	EBF1	chr15:38856977-38857481	GM12878	blood:	n/a	chr15:38857211-38857224 chr15:38857325-38857334 chr15:38857213-38857223 chr15:38857323-38857336 chr15:38857212-38857223

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	chr15:38855739..38857440-chr15:38962653..38964526,2	MCF-7	breast:
4	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
ENSG00000259747	Chromatin interaction

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

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:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38853600-38857600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:38855000-38857800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:38855400-38857400	Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr15:38855400-38857600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:38855600-38857800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr15:38855800-38857600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:38855800-38857600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:38856000-38857400	Active TSS	Fetal Kidney	kidney
9	chr15:38856000-38857600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr15:38856000-38857600	Active TSS	A549	lung
11	chr15:38856000-38857800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr15:38856000-38857800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr15:38856000-38857800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr15:38856200-38857400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:38856200-38857400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:38856200-38857400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:38856200-38857400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:38856200-38857400	Bivalent/Poised TSS	HSMM	muscle
19	chr15:38856200-38857400	Bivalent/Poised TSS	HSMMtube	muscle
20	chr15:38856200-38857400	Active TSS	K562	blood
21	chr15:38856200-38857600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:38856200-38857600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:38856200-38857600	Bivalent Enhancer	Fetal Lung	lung
24	chr15:38856200-38857800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
25	chr15:38856200-38857800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr15:38856200-38857800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr15:38856200-38857800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr15:38856400-38857400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr15:38856400-38857400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr15:38856400-38857400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr15:38856400-38857400	Bivalent/Poised TSS	Stomach Mucosa	stomach
32	chr15:38856400-38857400	Bivalent/Poised TSS	NHEK	skin
33	chr15:38856400-38857600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:38856400-38857600	Active TSS	Brain Angular Gyrus	brain
35	chr15:38856400-38857600	Active TSS	Brain Anterior Caudate	brain
36	chr15:38856400-38857600	Active TSS	Brain Hippocampus Middle	brain
37	chr15:38856400-38857600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr15:38856400-38857600	Active TSS	Fetal Brain Female	brain
39	chr15:38856400-38857800	Active TSS	Brain Cingulate Gyrus	brain
40	chr15:38856600-38857400	Bivalent/Poised TSS	NH-A	brain
41	chr15:38856800-38857400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
42	chr15:38857000-38857400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:38857000-38857400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:38857000-38857400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr15:38857000-38857400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:38857000-38857400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:38857000-38857400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:38857000-38857400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
49	chr15:38857000-38857400	Flanking Active TSS	Liver	Liver
50	chr15:38857000-38857400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland

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