Variant report

Variant	rs185400252
Chromosome Location	chr15:75493238-75493239
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	ELF1	chr15:75492615-75496148	GM12878	blood:	n/a	chr15:75494140-75494152 chr15:75495499-75495512 chr15:75494019-75494031 chr15:75493189-75493202 chr15:75495186-75495195 chr15:75495209-75495220 chr15:75494372-75494384 chr15:75493163-75493175 chr15:75493191-75493202 chr15:75495210-75495219
2	POLR2A	chr15:75492953-75496691	GM19193	blood:	n/a	n/a
3	RUNX3	chr15:75492986-75496547	GM12878	blood:	n/a	n/a
4	JUND	chr15:75493061-75493324	H1-hESC	embryonic stem cell:	n/a	chr15:75493171-75493180 chr15:75493291-75493302
5	SPI1	chr15:75492920-75493473	HL-60	blood:	n/a	chr15:75493191-75493200 chr15:75493190-75493203 chr15:75493402-75493415 chr15:75493189-75493202 chr15:75493192-75493199 chr15:75493190-75493203
6	CREB1	chr15:75492940-75493492	HepG2	liver:	n/a	n/a
7	TEAD4	chr15:75492986-75494085	K562	blood:	n/a	n/a
8	POLR2A	chr15:75492994-75495447	Hela-S3	cervix:	n/a	n/a
9	GABPA	chr15:75493046-75493341	HepG2	liver:	n/a	n/a
10	TCF7L2	chr15:75493199-75494104	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr15:75493126-75493403	MCF10A-Er-Src	breast:	n/a	chr15:75493377-75493389 chr15:75493256-75493270
12	POLR2A	chr15:75492412-75497603	GM18505	blood:	n/a	n/a
13	PRDM1	chr15:75493172-75493364	Hela-S3	cervix:	n/a	n/a
14	EGR1	chr15:75492798-75493561	HCT-116	colon:	n/a	chr15:75493165-75493175 chr15:75493190-75493199 chr15:75493252-75493276 chr15:75493165-75493178 chr15:75493164-75493179 chr15:75493162-75493176 chr15:75493164-75493178 chr15:75493165-75493178 chr15:75493165-75493178 chr15:75493166-75493176 chr15:75493160-75493182 chr15:75493165-75493178 chr15:75493166-75493175
15	POLR2A	chr15:75492653-75493781	GM12878	blood:	n/a	n/a
16	RCOR1	chr15:75493046-75493438	K562	blood:	n/a	n/a
17	RCOR1	chr15:75492800-75495327	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr15:75490327-75497524	GM12891	blood:	n/a	n/a
19	CHD2	chr15:75493065-75493591	Hela-S3	cervix:	n/a	chr15:75493160-75493170
20	TCF3	chr15:75493073-75493511	GM12878	blood:	n/a	chr15:75493366-75493380 chr15:75493394-75493408 chr15:75493235-75493248
21	HNF4A	chr15:75493199-75493471	HepG2	liver:	n/a	chr15:75493354-75493367 chr15:75493355-75493367 chr15:75493355-75493368 chr15:75493353-75493368 chr15:75493354-75493368 chr15:75493355-75493368 chr15:75493350-75493372 chr15:75493355-75493367
22	TFAP2C	chr15:75492839-75495794	Hela-S3	cervix:	n/a	chr15:75494924-75494939
23	EP300	chr15:75492823-75495560	ECC-1	luminal epithelium:	n/a	chr15:75493187-75493201 chr15:75494420-75494429 chr15:75494529-75494545 chr15:75495184-75495193 chr15:75494447-75494456 chr15:75494478-75494494 chr15:75495183-75495192 chr15:75492831-75492840 chr15:75494803-75494812 chr15:75493191-75493200 chr15:75494063-75494079 chr15:75494226-75494242
24	GABPA	chr15:75492816-75493508	MCF-7	breast:	n/a	n/a
25	SMARCC1	chr15:75492612-75494097	Hela-S3	cervix:	n/a	n/a
26	SPI1	chr15:75493087-75493303	K562	blood:	n/a	chr15:75493191-75493200 chr15:75493190-75493203 chr15:75493189-75493202 chr15:75493192-75493199 chr15:75493190-75493203
27	POLR2A	chr15:75493146-75493425	HepG2	liver:	n/a	n/a
28	POLR2A	chr15:75493101-75493759	ECC-1	luminal epithelium:	n/a	n/a
29	STAT5A	chr15:75492643-75496896	GM12878	blood:	n/a	chr15:75496563-75496577 chr15:75496565-75496574 chr15:75495565-75495576 chr15:75493377-75493389 chr15:75496566-75496575 chr15:75493549-75493557 chr15:75496045-75496057 chr15:75493256-75493270
30	POLR2A	chr15:75493161-75493388	HepG2	liver:	n/a	n/a
31	POU2F2	chr15:75493073-75495954	GM12878	blood:	n/a	chr15:75493166-75493178 chr15:75495907-75495919
32	POLR2A	chr15:75492939-75493432	HCT-116	colon:	n/a	n/a
33	MYC	chr15:75493134-75493313	K562	blood:	n/a	n/a
34	TCF12	chr15:75493008-75496156	A549	lung:	n/a	chr15:75493235-75493245 chr15:75493370-75493380 chr15:75493548-75493556
35	CTCF	chr15:75493174-75496126	A549	lung:	n/a	chr15:75495837-75495855 chr15:75495839-75495852 chr15:75495188-75495201
36	POLR2A	chr15:75493073-75496869	Hela-S3	cervix:	n/a	n/a
37	TCF12	chr15:75492891-75495553	ECC-1	luminal epithelium:	n/a	chr15:75492906-75492916 chr15:75493235-75493245 chr15:75493370-75493380 chr15:75493548-75493556
38	POLR2A	chr15:75492753-75495273	ECC-1	luminal epithelium:	n/a	n/a
39	GABPA	chr15:75493092-75493324	HepG2	liver:	n/a	n/a
40	FOS	chr15:75492975-75493393	MCF10A-Er-Src	breast:	n/a	chr15:75493171-75493180 chr15:75493291-75493302
41	JUN	chr15:75493130-75493362	H1-hESC	embryonic stem cell:	n/a	chr15:75493171-75493180 chr15:75493291-75493302
42	SMC3	chr15:75492813-75495936	Hela-S3	cervix:	n/a	chr15:75494800-75494810
43	POLR2A	chr15:75492560-75493801	GM12878	blood:	n/a	n/a
44	ELF1	chr15:75492988-75493519	HepG2	liver:	n/a	chr15:75493189-75493202 chr15:75493163-75493175 chr15:75493191-75493202
45	POLR2A	chr15:75493213-75493430	GM12891	blood:	n/a	n/a
46	ZEB1	chr15:75492954-75494012	GM12878	blood:	n/a	chr15:75493396-75493407 chr15:75493396-75493407
47	MYC	chr15:75492916-75495370	Hela-S3	cervix:	n/a	chr15:75494093-75494102
48	MAX	chr15:75492971-75495582	HepG2	liver:	n/a	chr15:75494093-75494102
49	CREB1	chr15:75492886-75493486	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAZ	chr15:75492986-75495484	Hela-S3	cervix:	n/a	chr15:75494093-75494102

No.	Distal block	Cell Line	Cell type
1	chr15:75314737..75326433-chr15:75490770..75500610,30	K562	blood:
2	chr15:75470196..75472288-chr15:75492167..75494098,2	K562	blood:
3	chr15:75312886..75327225-chr15:75491522..75500922,36	K562	blood:
4	chr15:75314704..75323577-chr15:75491522..75500562,29	MCF-7	breast:
5	chr15:75334055..75342899-chr15:75492444..75498798,20	K562	blood:
6	chr15:75333855..75341122-chr15:75492635..75495814,9	MCF-7	breast:
7	chr15:75314427..75332274-chr15:75491598..75502885,56	MCF-7	breast:
8	chr15:75405088..75407275-chr15:75491436..75494556,3	MCF-7	breast:
9	chr15:75487202..75491376-chr15:75491587..75495203,5	K562	blood:
10	chr15:75307941..75311039-chr15:75492807..75495397,4	MCF-7	breast:
11	chr15:75331603..75340227-chr15:75492938..75499942,15	K562	blood:
12	chr15:75486189..75488237-chr15:75491823..75494086,2	MCF-7	breast:
13	chr15:75490684..75493339-chr15:75497415..75499804,2	K562	blood:
14	chr15:75492389..75494597-chr8:145752169..145754298,2	MCF-7	breast:
15	chr15:74906571..74908107-chr15:75493036..75494786,2	MCF-7	breast:
16	chr15:75488848..75492298-chr15:75492406..75495739,4	MCF-7	breast:
17	chr15:75477700..75479387-chr15:75492353..75494507,2	MCF-7	breast:
18	chr15:75332512..75342228-chr15:75491817..75496419,22	MCF-7	breast:

Variant related genes	Relation type
C15orf39	TF binding region
ENSG00000254402	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000213563	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000167173	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000260152	Chromatin interaction
ENSG00000240366	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000260483	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904383	chr15:75382542-75520378	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1796196	chr15:75389382-75531124	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv1053212	chr15:75428467-75534408	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv833056	chr15:75452947-75614590	Enhancers Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	esv3422174	chr15:75492924-75495772	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75488200-75493400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr15:75488600-75493400	Weak transcription	Ovary	ovary
3	chr15:75491000-75493400	Weak transcription	Brain Anterior Caudate	brain
4	chr15:75491200-75493600	Enhancers	Lung	lung
5	chr15:75491200-75494000	Flanking Active TSS	GM12878-XiMat	blood
6	chr15:75491200-75494000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr15:75491400-75493400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:75491800-75493400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:75491800-75493400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr15:75492000-75493400	Enhancers	Brain Hippocampus Middle	brain
11	chr15:75492000-75493400	Enhancers	Dnd41	blood
12	chr15:75492000-75493600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:75492200-75493400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:75492200-75493400	Enhancers	Right Ventricle	heart
15	chr15:75492200-75493600	Enhancers	Left Ventricle	heart
16	chr15:75492200-75494000	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr15:75492400-75493400	Enhancers	Stomach Smooth Muscle	stomach
18	chr15:75492400-75493600	Enhancers	Right Atrium	heart
19	chr15:75492400-75494000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr15:75492400-75494000	Flanking Active TSS	Hela-S3	cervix
21	chr15:75492600-75493400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:75492600-75493400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:75492600-75493400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr15:75492600-75493400	Enhancers	Spleen	Spleen
25	chr15:75492600-75493600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:75492600-75493600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr15:75492600-75493600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:75492600-75493800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:75492600-75493800	Bivalent Enhancer	Fetal Brain Male	brain
30	chr15:75492600-75494000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr15:75492600-75494000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:75492600-75494000	Flanking Active TSS	Fetal Intestine Large	intestine
33	chr15:75492600-75494000	Flanking Active TSS	Fetal Intestine Small	intestine
34	chr15:75492600-75494000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr15:75492600-75494200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr15:75492600-75494200	Flanking Active TSS	NHEK	skin
37	chr15:75492800-75493400	Bivalent Enhancer	Fetal Muscle Leg	muscle
38	chr15:75492800-75493400	Enhancers	Psoas Muscle	Psoas
39	chr15:75492800-75493800	Flanking Active TSS	Colonic Mucosa	Colon
40	chr15:75492800-75494000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:75492800-75494000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr15:75492800-75494000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:75492800-75494000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:75492800-75494000	Flanking Active TSS	Placenta	Placenta
45	chr15:75492800-75494000	Flanking Active TSS	HMEC	breast
46	chr15:75492800-75495800	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr15:75492800-75495800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr15:75492800-75496800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr15:75493000-75493400	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr15:75493000-75493600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links