Variant report

Variant	rs534519246
Chromosome Location	chr15:40212661-40212662
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	CTBP2	chr15:40211745-40213391	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:40212212-40213492	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:40211939-40213593	U87	brain:	n/a	n/a
4	MAX	chr15:40212053-40213564	SK-N-SH	brain:	n/a	chr15:40212599-40212609 chr15:40213170-40213189 chr15:40213173-40213186 chr15:40213175-40213184 chr15:40213173-40213186 chr15:40213175-40213184
5	POLR2A	chr15:40212050-40212718	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chr15:40212512-40212666	SK-N-SH_RA	brain:	n/a	n/a
7	MAX	chr15:40211842-40213891	A549	lung:	n/a	chr15:40211866-40211875 chr15:40212599-40212609 chr15:40213170-40213189 chr15:40213173-40213186 chr15:40213175-40213184 chr15:40213173-40213186 chr15:40213175-40213184
8	CTCF	chr15:40212450-40212708	NHEK	skin:	n/a	chr15:40212458-40212476 chr15:40212461-40212474 chr15:40212460-40212481
9	TBP	chr15:40212070-40213435	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:40211934-40213607	ProgFib	skin:	n/a	n/a
11	USF1	chr15:40212041-40213617	SK-N-SH	brain:	n/a	chr15:40213173-40213186 chr15:40212409-40212425 chr15:40213173-40213184 chr15:40213205-40213221 chr15:40213143-40213159 chr15:40213213-40213229
12	CTCF	chr15:40212560-40212710	NHLF	lung:	n/a	n/a
13	POLR2A	chr15:40212119-40212828	SK-N-SH	brain:	n/a	n/a
14	STAT5A	chr15:40212600-40213478	GM12878	blood:	n/a	n/a
15	CTCF	chr15:40212580-40212730	HBMEC	blood vessel:	n/a	n/a
16	BACH1	chr15:40212357-40213516	H1-hESC	embryonic stem cell:	n/a	n/a
17	USF2	chr15:40212371-40213410	H1-hESC	embryonic stem cell:	n/a	chr15:40213173-40213184 chr15:40213173-40213186 chr15:40212409-40212425 chr15:40213205-40213221 chr15:40213143-40213159 chr15:40213213-40213229
18	RAD21	chr15:40211713-40213724	IMR90	lung:	n/a	chr15:40212460-40212474 chr15:40213138-40213152 chr15:40212463-40212472 chr15:40212459-40212478
19	CTCF	chr15:40212540-40212690	HBMEC	blood vessel:	n/a	n/a
20	POLR2A	chr15:40212288-40213441	H1-hESC	embryonic stem cell:	n/a	n/a
21	TCF7L2	chr15:40212290-40212824	PANC-1	pancreas:	n/a	n/a
22	CTCF	chr15:40212540-40212690	RPTEC	kidney:	n/a	n/a
23	MAX	chr15:40212415-40213603	Hela-S3	cervix:	n/a	chr15:40212599-40212609 chr15:40213170-40213189 chr15:40213173-40213186 chr15:40213175-40213184 chr15:40213173-40213186 chr15:40213175-40213184
24	SIN3A	chr15:40210791-40213517	H1-hESC	embryonic stem cell:	n/a	chr15:40212876-40212887 chr15:40211973-40211984 chr15:40213174-40213183
25	E2F6	chr15:40211968-40213612	H1-hESC	embryonic stem cell:	n/a	chr15:40212251-40212260 chr15:40213151-40213160 chr15:40212313-40212323 chr15:40212394-40212403 chr15:40212410-40212419 chr15:40212983-40212990
26	POLR2A	chr15:40211977-40213513	H1-hESC	embryonic stem cell:	n/a	n/a
27	MXI1	chr15:40210471-40214149	IMR90	lung:	n/a	chr15:40213174-40213183
28	MAX	chr15:40211905-40213554	HepG2	liver:	n/a	chr15:40212599-40212609 chr15:40213170-40213189 chr15:40213173-40213186 chr15:40213175-40213184 chr15:40213173-40213186 chr15:40213175-40213184
29	MAX	chr15:40211902-40213610	ECC-1	luminal epithelium:	n/a	chr15:40212599-40212609 chr15:40213170-40213189 chr15:40213173-40213186 chr15:40213175-40213184 chr15:40213173-40213186 chr15:40213175-40213184
30	NFIC	chr15:40212218-40213727	ECC-1	luminal epithelium:	n/a	chr15:40212879-40212896 chr15:40212880-40212896
31	E2F6	chr15:40212296-40212747	A549	lung:	n/a	chr15:40212313-40212323 chr15:40212394-40212403 chr15:40212410-40212419
32	SIN3AK20	chr15:40211952-40213434	PANC-1	pancreas:	n/a	n/a
33	POLR2A	chr15:40211913-40213552	Gliobla	brain:	n/a	n/a
34	POLR2A	chr15:40212055-40213752	SK-N-MC	brain:	n/a	n/a
35	CTCF	chr15:40212560-40212710	HRPEpiC	eye:	n/a	n/a
36	CTCF	chr15:40212600-40212750	WI-38	lung:	n/a	n/a
37	SIN3AK20	chr15:40211931-40213250	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr15:40212560-40212710	GM12872	blood:	n/a	n/a
39	MAX	chr15:40212073-40213690	ECC-1	luminal epithelium:	n/a	chr15:40212599-40212609 chr15:40213170-40213189 chr15:40213173-40213186 chr15:40213175-40213184 chr15:40213173-40213186 chr15:40213175-40213184
40	POLR2A	chr15:40212286-40213405	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAX	chr15:40211966-40213569	SK-N-SH	brain:	n/a	chr15:40212599-40212609 chr15:40213170-40213189 chr15:40213173-40213186 chr15:40213175-40213184 chr15:40213173-40213186 chr15:40213175-40213184
42	CTCF	chr15:40212456-40212821	ProgFib	skin:	n/a	chr15:40212458-40212476 chr15:40212461-40212474 chr15:40212460-40212481
43	CTCF	chr15:40212520-40212670	AoAF	blood vessel:	n/a	n/a
44	POLR2A	chr15:40212011-40213698	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr15:40212540-40212690	HA-sp	spinal cord:	n/a	n/a
46	CTCF	chr15:40212520-40212670	AG04449	skin:	n/a	n/a
47	ZBTB7A	chr15:40212082-40213542	ECC-1	luminal epithelium:	n/a	chr15:40213008-40213017
48	CTCF	chr15:40212445-40212729	A549	lung:	n/a	chr15:40212458-40212476 chr15:40212461-40212474 chr15:40212460-40212481
49	CTCF	chr15:40212560-40212710	AG10803	skin:	n/a	n/a
50	MYC	chr15:40212402-40212673	HUVEC	blood vessel:	n/a	chr15:40212599-40212609

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40211366..40214080-chr15:40223428..40228644,6	MCF-7	breast:
2	chr15:40211846..40214390-chr15:40224576..40226655,2	K562	blood:

Variant related genes	Relation type
GPR176	TF binding region
ENSG00000246863	TF binding region
ENSG00000128829	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv832983	chr15:40098766-40248839	Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv3388242	chr15:40210910-40214408	Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
5	esv3374779	chr15:40211885-40214433	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40209200-40213400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr15:40209200-40213800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr15:40209800-40213800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr15:40210000-40213600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr15:40210200-40212800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr15:40210200-40213600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr15:40210200-40213600	Active TSS	NHLF	lung
8	chr15:40210400-40212800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr15:40210400-40213400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:40210400-40213400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:40210400-40213600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:40210400-40213600	Active TSS	Aorta	Aorta
13	chr15:40210400-40213800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:40210600-40212800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:40210600-40213000	Active TSS	NH-A	brain
16	chr15:40210600-40213800	Active TSS	HSMM	muscle
17	chr15:40210800-40212800	Active TSS	Muscle Satellite Cultured Cells	--
18	chr15:40210800-40213400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:40210800-40213400	Active TSS	HSMMtube	muscle
20	chr15:40210800-40213600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:40210800-40213600	Active TSS	NHDF-Ad	bronchial
22	chr15:40210800-40213800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:40211000-40212800	Bivalent/Poised TSS	Fetal Brain Female	brain
24	chr15:40211000-40213000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
25	chr15:40211000-40213400	Active TSS	Osteobl	bone
26	chr15:40211000-40213600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:40211000-40213600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:40211000-40213600	Active TSS	Brain Anterior Caudate	brain
29	chr15:40211200-40213000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:40211200-40213600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:40211200-40213600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:40211200-40213800	Active TSS	Brain Angular Gyrus	brain
33	chr15:40211200-40213800	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr15:40211400-40212800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
35	chr15:40211400-40212800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
36	chr15:40211400-40213400	Active TSS	NHEK	skin
37	chr15:40211600-40212800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
38	chr15:40211600-40212800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
39	chr15:40211600-40213000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
40	chr15:40211600-40213000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:40211600-40213000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
42	chr15:40211600-40213000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
43	chr15:40211600-40213000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
44	chr15:40211600-40213400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:40211600-40213400	Active TSS	Hela-S3	cervix
46	chr15:40211600-40213600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:40211600-40213800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:40211800-40212800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
49	chr15:40211800-40212800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
50	chr15:40211800-40212800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links