Variant report

Variant	rs544377689
Chromosome Location	chr15:38856028-38856029
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	TBL1XR1	chr15:38856024-38856386	K562	blood:	n/a	n/a
2	CTCF	chr15:38855965-38856162	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:38855527-38857241	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:38852140-38857375	GM12878	blood:	n/a	n/a
5	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
6	CTCF	chr15:38856012-38856096	A549	lung:	n/a	n/a
7	MTA3	chr15:38855988-38856709	GM12878	blood:	n/a	n/a
8	MAZ	chr15:38855705-38857330	IMR90	lung:	n/a	chr15:38856887-38856897
9	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
10	WRNIP1	chr15:38854370-38856578	GM12878	blood:	n/a	n/a
11	CTCF	chr15:38856020-38856814	A549	lung:	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
12	CTCF	chr15:38855929-38856197	GM19238	blood:	n/a	n/a
13	POLR2A	chr15:38855482-38857322	GM12878	blood:	n/a	n/a
14	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
15	CTCF	chr15:38855900-38856050	GM12872	blood:	n/a	n/a
16	POLR2A	chr15:38855773-38857651	Raji	blood:	n/a	n/a
17	POLR2A	chr15:38855775-38857469	GM15510	blood:	n/a	n/a
18	CTCF	chr15:38856008-38856139	Fibrobl	skin:	n/a	n/a
19	POLR2A	chr15:38855908-38856118	MCF-7	breast:	n/a	n/a
20	POLR2A	chr15:38855836-38857229	GM12878	blood:	n/a	n/a
21	RUNX3	chr15:38855944-38856655	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:38855838-38856615	GM12891	blood:	n/a	n/a
23	CTCF	chr15:38856011-38856106	MCF-7	breast:	n/a	n/a
24	CHD1	chr15:38854483-38857484	GM12878	blood:	n/a	chr15:38857153-38857163
25	POLR2A	chr15:38855485-38857360	GM12892	blood:	n/a	n/a
26	STAT1	chr15:38855932-38856577	GM12878	blood:	n/a	chr15:38856489-38856496 chr15:38856376-38856388
27	POLR2A	chr15:38853749-38857329	GM18505	blood:	n/a	n/a
28	RELA	chr15:38855308-38857242	GM15510	blood:	n/a	n/a
29	POLR2A	chr15:38855478-38856699	GM12878	blood:	n/a	n/a
30	RELA	chr15:38854563-38856656	GM19099	blood:	n/a	n/a
31	MAX	chr15:38855945-38856583	GM12878	blood:	n/a	n/a
32	EBF1	chr15:38855052-38856583	GM12878	blood:	n/a	n/a
33	CTCF	chr15:38856003-38856138	ProgFib	skin:	n/a	n/a
34	CTCF	chr15:38855927-38856143	GM12891	blood:	n/a	n/a
35	SMC3	chr15:38855281-38856708	GM12878	blood:	n/a	chr15:38856386-38856400 chr15:38856388-38856402 chr15:38856388-38856395 chr15:38856392-38856402
36	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
37	POLR2A	chr15:38856024-38856085	MCF-7	breast:	n/a	n/a
38	CTCF	chr15:38855920-38856070	NHLF	lung:	n/a	n/a
39	POLR2A	chr15:38855571-38856645	GM12891	blood:	n/a	n/a
40	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
41	BHLHE40	chr15:38856013-38856625	GM12878	blood:	n/a	chr15:38856424-38856440
42	POLR2A	chr15:38854455-38857370	GM19099	blood:	n/a	n/a
43	NFATC1	chr15:38855955-38856686	GM12878	blood:	n/a	n/a
44	CTCF	chr15:38856026-38856095	Medullo	brain:	n/a	n/a
45	POLR2A	chr15:38855872-38857308	GM12878	blood:	n/a	n/a
46	RFX5	chr15:38855891-38856589	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:38854424-38857197	GM12878	blood:	n/a	n/a
48	CHD2	chr15:38855886-38857474	GM12878	blood:	n/a	chr15:38857153-38857163
49	POLR2A	chr15:38855463-38856663	GM12892	blood:	n/a	n/a
50	POLR2A	chr15:38855602-38857412	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:38842649..38844707-chr15:38853512..38856780,3	MCF-7	breast:
2	chr15:38732611..38733581-chr15:38855892..38856789,2	K562	blood:
3	chr15:38818335..38820661-chr15:38853754..38856224,2	MCF-7	breast:
4	chr15:38855957..38856812-chr15:38975562..38976269,2	MCF-7	breast:
5	chr15:38819782..38822261-chr15:38854232..38856732,2	MCF-7	breast:
6	chr15:38744991..38746966-chr15:38854872..38857693,2	MCF-7	breast:
7	chr14:20810314..20812793-chr15:38855404..38857234,2	MCF-7	breast:
8	chr15:38855739..38857440-chr15:38962653..38964526,2	MCF-7	breast:
9	chr15:38855983..38856775-chr15:38939446..38940179,2	MCF-7	breast:
10	chr15:38854703..38856718-chr15:38889732..38892126,2	MCF-7	breast:
11	chr15:38855702..38858314-chr15:38985984..38988881,2	MCF-7	breast:

Variant related genes	Relation type
RASGRP1	TF binding region
ENSG00000259001	Chromatin interaction
ENSG00000171262	Chromatin interaction
ENSG00000129484	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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38852000-38856200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr15:38852200-38856200	Flanking Active TSS	GM12878-XiMat	blood
3	chr15:38852400-38856200	Weak transcription	Right Atrium	heart
4	chr15:38853600-38856800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
5	chr15:38853600-38857600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:38854200-38856200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr15:38855000-38857000	Active TSS	Duodenum Mucosa	Duodenum
8	chr15:38855000-38857800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:38855200-38856400	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr15:38855200-38857200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:38855200-38857200	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr15:38855400-38857400	Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr15:38855400-38857600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:38855600-38856200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
15	chr15:38855600-38856400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr15:38855600-38856400	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr15:38855600-38856400	Flanking Active TSS	Dnd41	blood
18	chr15:38855600-38857200	Active TSS	Primary T cells from cord blood	blood
19	chr15:38855600-38857200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:38855600-38857800	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr15:38855800-38856200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
22	chr15:38855800-38856200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr15:38855800-38856200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:38855800-38856200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr15:38855800-38856200	Bivalent Enhancer	Fetal Intestine Large	intestine
26	chr15:38855800-38856200	Flanking Active TSS	Fetal Thymus	thymus
27	chr15:38855800-38856200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
28	chr15:38855800-38856400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:38855800-38856400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:38855800-38856400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:38855800-38856400	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr15:38855800-38856400	Flanking Active TSS	Brain Cingulate Gyrus	brain
33	chr15:38855800-38856400	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr15:38855800-38856400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr15:38855800-38856400	Flanking Active TSS	Esophagus	oesophagus
36	chr15:38855800-38856400	Bivalent Enhancer	Stomach Mucosa	stomach
37	chr15:38855800-38856600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
38	chr15:38855800-38856800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
39	chr15:38855800-38857000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
40	chr15:38855800-38857200	Active TSS	Small Intestine	intestine
41	chr15:38855800-38857600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:38855800-38857600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:38856000-38856200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
44	chr15:38856000-38856200	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:38856000-38856200	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
46	chr15:38856000-38856200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:38856000-38856200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:38856000-38856200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
49	chr15:38856000-38856200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
50	chr15:38856000-38856200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell

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