Variant report

Variant	rs546900680
Chromosome Location	chr15:38855870-38855871
allele	-/GAATC
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	POLR2A	chr15:38855527-38857241	GM12892	blood:	n/a	n/a
2	POLR2A	chr15:38852140-38857375	GM12878	blood:	n/a	n/a
3	CTCF	chr15:38855850-38856610	GM12878	blood:	n/a	chr15:38856420-38856428 chr15:38856386-38856404 chr15:38856391-38856401 chr15:38856386-38856399 chr15:38856389-38856402 chr15:38856389-38856402 chr15:38856388-38856409 chr15:38856389-38856398 chr15:38856387-38856403 chr15:38856379-38856392
4	MAZ	chr15:38855705-38857330	IMR90	lung:	n/a	chr15:38856887-38856897
5	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
6	WRNIP1	chr15:38854370-38856578	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:38855482-38857322	GM12878	blood:	n/a	n/a
8	SMC3	chr15:38855861-38857339	SK-N-SH	brain:	n/a	chr15:38856386-38856400 chr15:38856388-38856402 chr15:38856903-38856913 chr15:38856388-38856395 chr15:38856392-38856402
9	POLR2A	chr15:38855773-38857651	Raji	blood:	n/a	n/a
10	CTCF	chr15:38855760-38855910	HFF-Myc	foreskin:	n/a	n/a
11	POLR2A	chr15:38855775-38857469	GM15510	blood:	n/a	n/a
12	POLR2A	chr15:38855836-38857229	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:38855838-38856615	GM12891	blood:	n/a	n/a
14	CHD1	chr15:38854483-38857484	GM12878	blood:	n/a	chr15:38857153-38857163
15	POLR2A	chr15:38855485-38857360	GM12892	blood:	n/a	n/a
16	POLR2A	chr15:38853749-38857329	GM18505	blood:	n/a	n/a
17	RELA	chr15:38855308-38857242	GM15510	blood:	n/a	n/a
18	POLR2A	chr15:38855478-38856699	GM12878	blood:	n/a	n/a
19	CTCF	chr15:38855840-38855990	HEEpiC	esophagus:	n/a	n/a
20	RELA	chr15:38854563-38856656	GM19099	blood:	n/a	n/a
21	EBF1	chr15:38855052-38856583	GM12878	blood:	n/a	n/a
22	CTCF	chr15:38855720-38855870	GM12873	blood:	n/a	n/a
23	SMC3	chr15:38855281-38856708	GM12878	blood:	n/a	chr15:38856386-38856400 chr15:38856388-38856402 chr15:38856388-38856395 chr15:38856392-38856402
24	POLR2A	chr15:38855571-38856645	GM12891	blood:	n/a	n/a
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	CTCF	chr15:38855820-38855970	GM12864	blood:	n/a	n/a
28	POLR2A	chr15:38854424-38857197	GM12878	blood:	n/a	n/a
29	POLR2A	chr15:38855463-38856663	GM12892	blood:	n/a	n/a
30	POLR2A	chr15:38855602-38857412	GM18951	blood:	n/a	n/a
31	POLR2A	chr15:38855272-38857408	GM19193	blood:	n/a	n/a
32	RCOR1	chr15:38855607-38857283	IMR90	lung:	n/a	n/a
33	POLR2A	chr15:38855567-38856695	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:38855570-38857299	GM12892	blood:	n/a	n/a
35	POLR2A	chr15:38855692-38857399	GM12892	blood:	n/a	n/a
36	CTCF	chr15:38855860-38856010	HCPEpiC	choroid plexus:	n/a	n/a
37	RELA	chr15:38855452-38856626	GM18951	blood:	n/a	n/a
38	FOXM1	chr15:38855856-38856625	GM12878	blood:	n/a	n/a
39	CTBP2	chr15:38855868-38857758	H1-hESC	embryonic stem cell:	n/a	n/a
40	MXI1	chr15:38855693-38856610	GM12878	blood:	n/a	n/a
41	IKZF1	chr15:38855719-38856000	GM12878	blood:	n/a	n/a
42	MTA3	chr15:38855686-38856620	GM12878	blood:	n/a	n/a
43	RELA	chr15:38854546-38857248	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:38842649..38844707-chr15:38853512..38856780,3	MCF-7	breast:
2	chr15:38818335..38820661-chr15:38853754..38856224,2	MCF-7	breast:
3	chr15:38819782..38822261-chr15:38854232..38856732,2	MCF-7	breast:
4	chr15:38744991..38746966-chr15:38854872..38857693,2	MCF-7	breast:
5	chr14:20810314..20812793-chr15:38855404..38857234,2	MCF-7	breast:
6	chr15:38855739..38857440-chr15:38962653..38964526,2	MCF-7	breast:
7	chr15:38854703..38856718-chr15:38889732..38892126,2	MCF-7	breast:
8	chr15:38855702..38858314-chr15:38985984..38988881,2	MCF-7	breast:

Variant related genes	Relation type
RASGRP1	TF binding region
ENSG00000259001	Chromatin interaction
ENSG00000259747	Chromatin interaction
ENSG00000171262	Chromatin interaction
ENSG00000175779	Chromatin interaction
ENSG00000129484	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:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38851200-38856000	Weak transcription	Lung	lung
2	chr15:38852000-38856000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:38852000-38856200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr15:38852200-38856200	Flanking Active TSS	GM12878-XiMat	blood
5	chr15:38852400-38856200	Weak transcription	Right Atrium	heart
6	chr15:38852600-38856000	Weak transcription	Fetal Heart	heart
7	chr15:38853600-38856800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
8	chr15:38853600-38857600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:38854200-38856000	Flanking Active TSS	Thymus	Thymus
10	chr15:38854200-38856200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
11	chr15:38855000-38857000	Active TSS	Duodenum Mucosa	Duodenum
12	chr15:38855000-38857800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:38855200-38856000	Active TSS	Brain Anterior Caudate	brain
14	chr15:38855200-38856400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr15:38855200-38857200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:38855200-38857200	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr15:38855400-38856000	Enhancers	Primary hematopoietic stem cells	blood
18	chr15:38855400-38856000	Weak transcription	Spleen	Spleen
19	chr15:38855400-38857400	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr15:38855400-38857600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:38855600-38856000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:38855600-38856200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
23	chr15:38855600-38856400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr15:38855600-38856400	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr15:38855600-38856400	Flanking Active TSS	Dnd41	blood
26	chr15:38855600-38857200	Active TSS	Primary T cells from cord blood	blood
27	chr15:38855600-38857200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:38855600-38857800	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr15:38855800-38856000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:38855800-38856000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:38855800-38856000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr15:38855800-38856000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr15:38855800-38856000	Enhancers	Liver	Liver
34	chr15:38855800-38856000	Enhancers	Brain Substantia Nigra	brain
35	chr15:38855800-38856000	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr15:38855800-38856000	Active TSS	Fetal Brain Female	brain
37	chr15:38855800-38856000	Bivalent Enhancer	Placenta	Placenta
38	chr15:38855800-38856000	Enhancers	Pancreas	Pancrea
39	chr15:38855800-38856000	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr15:38855800-38856000	Bivalent Enhancer	Hela-S3	cervix
41	chr15:38855800-38856200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
42	chr15:38855800-38856200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr15:38855800-38856200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:38855800-38856200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr15:38855800-38856200	Bivalent Enhancer	Fetal Intestine Large	intestine
46	chr15:38855800-38856200	Flanking Active TSS	Fetal Thymus	thymus
47	chr15:38855800-38856200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
48	chr15:38855800-38856400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:38855800-38856400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:38855800-38856400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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