Variant report

Variant	rs80309120
Chromosome Location	chr15:38856818-38856819
allele	C/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	POLR2A	chr15:38856815-38857222	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr15:38856803-38857106	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr15:38856787-38857304	GM12878	blood:	n/a	n/a
5	MAX	chr15:38856762-38857289	HepG2	liver:	n/a	chr15:38856887-38856897
6	TAF1	chr15:38856713-38857228	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr15:38856783-38857685	H1-hESC	embryonic stem cell:	n/a	chr15:38856887-38856897
8	POLR2A	chr15:38855527-38857241	GM12892	blood:	n/a	n/a
9	POLR2A	chr15:38852140-38857375	GM12878	blood:	n/a	n/a
10	E2F6	chr15:38856262-38857249	K562	blood:	n/a	chr15:38857012-38857021
11	POLR2A	chr15:38856703-38857231	GM12891	blood:	n/a	n/a
12	POLR2A	chr15:38856259-38857623	MCF-7	breast:	n/a	n/a
13	MAX	chr15:38856735-38857351	HCT-116	colon:	n/a	chr15:38856887-38856897
14	MAZ	chr15:38855705-38857330	IMR90	lung:	n/a	chr15:38856887-38856897
15	CTCF	chr15:38856179-38857210	IMR90	lung:	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
16	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
17	MAX	chr15:38856809-38857274	A549	lung:	n/a	chr15:38856887-38856897
18	CTCF	chr15:38856743-38857182	GM19239	blood:	n/a	chr15:38856903-38856916
19	POLR2A	chr15:38855482-38857322	GM12878	blood:	n/a	n/a
20	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
21	TCF3	chr15:38856759-38857345	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:38855773-38857651	Raji	blood:	n/a	n/a
23	SIN3A	chr15:38856782-38857175	GM12878	blood:	n/a	chr15:38857098-38857109 chr15:38856867-38856878
24	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
25	MAZ	chr15:38856124-38857327	GM12878	blood:	n/a	chr15:38856887-38856897
26	POLR2A	chr15:38855775-38857469	GM15510	blood:	n/a	n/a
27	POLR2A	chr15:38855836-38857229	GM12878	blood:	n/a	n/a
28	MAX	chr15:38856804-38857203	K562	blood:	n/a	chr15:38856887-38856897
29	CCNT2	chr15:38856278-38857274	K562	blood:	n/a	chr15:38856682-38856691
30	RUNX3	chr15:38856775-38857234	GM12878	blood:	n/a	n/a
31	SIN3A	chr15:38856786-38857325	H1-hESC	embryonic stem cell:	n/a	chr15:38857098-38857109 chr15:38856867-38856878
32	UBTF	chr15:38856177-38857261	K562	blood:	n/a	n/a
33	HCFC1	chr15:38856254-38857153	K562	blood:	n/a	n/a
34	RAD21	chr15:38856152-38857310	H1-hESC	embryonic stem cell:	n/a	chr15:38856388-38856402 chr15:38856386-38856400 chr15:38856388-38856397 chr15:38856392-38856404 chr15:38856387-38856406
35	POLR2A	chr15:38856812-38857124	ECC-1	luminal epithelium:	n/a	n/a
36	CHD1	chr15:38854483-38857484	GM12878	blood:	n/a	chr15:38857153-38857163
37	MAX	chr15:38856797-38857220	HepG2	liver:	n/a	chr15:38856887-38856897
38	POLR2A	chr15:38855485-38857360	GM12892	blood:	n/a	n/a
39	E2F6	chr15:38856720-38857758	H1-hESC	embryonic stem cell:	n/a	chr15:38857340-38857347 chr15:38857012-38857021 chr15:38857340-38857347 chr15:38857340-38857347
40	PAX5	chr15:38856801-38857323	GM12878	blood:	n/a	chr15:38857032-38857041 chr15:38857030-38857039 chr15:38857008-38857017
41	MAX	chr15:38856798-38857315	HCT-116	colon:	n/a	chr15:38856887-38856897
42	POLR2A	chr15:38856777-38857228	GM12892	blood:	n/a	n/a
43	RAD21	chr15:38856804-38857129	GM12878	blood:	n/a	n/a
44	POLR2A	chr15:38853749-38857329	GM18505	blood:	n/a	n/a
45	EBF1	chr15:38856677-38857524	GM12878	blood:	n/a	chr15:38857211-38857224 chr15:38857325-38857334 chr15:38857213-38857223 chr15:38857323-38857336 chr15:38857212-38857223
46	RELA	chr15:38855308-38857242	GM15510	blood:	n/a	n/a
47	MAX	chr15:38856751-38857755	H1-hESC	embryonic stem cell:	n/a	chr15:38856887-38856897
48	MAX	chr15:38856768-38857221	K562	blood:	n/a	chr15:38856887-38856897
49	CTCF	chr15:38856188-38857168	K562	blood:	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
50	MAX	chr15:38856698-38857355	ECC-1	luminal epithelium:	n/a	chr15:38856887-38856897

No.	Distal block	Cell Line	Cell type
1	chr15:38744991..38746966-chr15:38854872..38857693,2	MCF-7	breast:
2	chr14:20810314..20812793-chr15:38855404..38857234,2	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
ENSG00000129484	Chromatin interaction
ENSG00000259747	Chromatin interaction
ENSG00000175779	Chromatin interaction
ENSG00000171262	Chromatin interaction
ENSG00000259001	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:125 , 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	chr15:38855000-38857000	Active TSS	Duodenum Mucosa	Duodenum
3	chr15:38855000-38857800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr15:38855200-38857200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:38855200-38857200	Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr15:38855400-38857400	Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr15:38855400-38857600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:38855600-38857200	Active TSS	Primary T cells from cord blood	blood
9	chr15:38855600-38857200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:38855600-38857800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr15:38855800-38857000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
12	chr15:38855800-38857200	Active TSS	Small Intestine	intestine
13	chr15:38855800-38857600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:38855800-38857600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:38856000-38857000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
16	chr15:38856000-38857200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:38856000-38857200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:38856000-38857200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:38856000-38857200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
20	chr15:38856000-38857200	Active TSS	Gastric	stomach
21	chr15:38856000-38857200	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr15:38856000-38857200	Active TSS	Thymus	Thymus
23	chr15:38856000-38857200	Bivalent/Poised TSS	Osteobl	bone
24	chr15:38856000-38857400	Active TSS	Fetal Kidney	kidney
25	chr15:38856000-38857600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr15:38856000-38857600	Active TSS	A549	lung
27	chr15:38856000-38857800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
28	chr15:38856000-38857800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr15:38856000-38857800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr15:38856200-38857000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:38856200-38857000	Active TSS	Colonic Mucosa	Colon
32	chr15:38856200-38857000	Active TSS	Hela-S3	cervix
33	chr15:38856200-38857000	Bivalent/Poised TSS	HepG2	liver
34	chr15:38856200-38857000	Bivalent/Poised TSS	NHLF	lung
35	chr15:38856200-38857200	Active TSS	H9 Cell Line	embryonic stem cell
36	chr15:38856200-38857200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:38856200-38857200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr15:38856200-38857200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:38856200-38857200	Active TSS	Primary T cells fromperipheralblood	blood
40	chr15:38856200-38857200	Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr15:38856200-38857200	Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr15:38856200-38857200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr15:38856200-38857200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
44	chr15:38856200-38857200	Active TSS	Brain Substantia Nigra	brain
45	chr15:38856200-38857200	Active TSS	Fetal Thymus	thymus
46	chr15:38856200-38857200	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr15:38856200-38857200	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr15:38856200-38857200	Active TSS	Right Ventricle	heart
49	chr15:38856200-38857200	Active TSS	GM12878-XiMat	blood
50	chr15:38856200-38857200	Bivalent/Poised TSS	HUVEC	blood vessel

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