Variant report

Variant	rs555318851
Chromosome Location	chr6:4775867-4775868
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	EGR1	chr6:4775737-4776045	GM12878	blood:	n/a	chr6:4775822-4775832 chr6:4775899-4775913
2	TCF12	chr6:4775217-4776392	ECC-1	luminal epithelium:	n/a	chr6:4775769-4775779 chr6:4775743-4775751
3	MAX	chr6:4774820-4776399	ECC-1	luminal epithelium:	n/a	chr6:4775819-4775828 chr6:4776302-4776311
4	POLR2A	chr6:4775427-4777680	NB4	blood:	n/a	n/a
5	POLR2A	chr6:4775593-4777225	A549	lung:	n/a	n/a
6	ELF1	chr6:4775022-4776356	GM12878	blood:	n/a	chr6:4775990-4776002 chr6:4776041-4776050
7	POLR2A	chr6:4774735-4775894	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr6:4775799-4776257	A549	lung:	n/a	chr6:4776012-4776022 chr6:4776196-4776205
9	PAX5	chr6:4775762-4776316	GM12892	blood:	n/a	chr6:4776137-4776146
10	POLR2A	chr6:4775604-4775979	HCT-116	colon:	n/a	n/a
11	POLR2A	chr6:4775740-4776370	HUVEC	blood vessel:	n/a	n/a
12	CEBPD	chr6:4775751-4776115	HepG2	liver:	n/a	n/a
13	SP1	chr6:4775396-4776924	HCT-116	colon:	n/a	chr6:4776388-4776399 chr6:4776322-4776334 chr6:4776322-4776334 chr6:4776376-4776387 chr6:4776322-4776333 chr6:4776012-4776022 chr6:4776196-4776205
14	MAX	chr6:4774967-4777723	HepG2	liver:	n/a	chr6:4775819-4775828 chr6:4776302-4776311 chr6:4777256-4777266 chr6:4777552-4777562
15	CHD2	chr6:4775581-4776727	GM12878	blood:	n/a	chr6:4775824-4775834
16	TAF1	chr6:4775458-4776352	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr6:4775007-4777491	MCF-7	breast:	n/a	n/a
18	POLR2A	chr6:4775632-4775873	A549	lung:	n/a	n/a
19	POLR2A	chr6:4775564-4775870	ECC-1	luminal epithelium:	n/a	n/a
20	NFIC	chr6:4775534-4776409	ECC-1	luminal epithelium:	n/a	n/a
21	SP1	chr6:4775646-4776882	HCT-116	colon:	n/a	chr6:4776388-4776399 chr6:4776322-4776334 chr6:4776322-4776334 chr6:4776376-4776387 chr6:4776322-4776333 chr6:4776012-4776022 chr6:4776196-4776205
22	MXI1	chr6:4775542-4776925	GM12878	blood:	n/a	chr6:4776030-4776039
23	MYC	chr6:4775646-4776397	A549	lung:	n/a	chr6:4775819-4775828 chr6:4776302-4776311
24	MAX	chr6:4775513-4776278	A549	lung:	n/a	chr6:4775819-4775828
25	POLR2A	chr6:4775557-4776945	MCF10A-Er-Src	breast:	n/a	n/a
26	RUNX3	chr6:4775587-4775947	GM12878	blood:	n/a	n/a
27	MAZ	chr6:4775403-4777742	GM12878	blood:	n/a	chr6:4775819-4775828 chr6:4776302-4776311 chr6:4777256-4777266
28	REST	chr6:4775779-4776001	SK-N-SH	brain:	n/a	chr6:4775824-4775834
29	POLR2A	chr6:4775555-4777837	GM15510	blood:	n/a	n/a
30	BHLHE40	chr6:4775622-4776738	GM12878	blood:	n/a	chr6:4776143-4776159 chr6:4776135-4776151 chr6:4775989-4776005 chr6:4775829-4775845
31	CREB1	chr6:4775487-4777065	HepG2	liver:	n/a	n/a
32	EP300	chr6:4775425-4776483	ECC-1	luminal epithelium:	n/a	chr6:4776041-4776050 chr6:4776082-4776098
33	POLR2A	chr6:4775668-4777730	GM18951	blood:	n/a	n/a
34	POLR2A	chr6:4775342-4777011	MCF-7	breast:	n/a	n/a
35	MAX	chr6:4775253-4776912	HCT-116	colon:	n/a	chr6:4775819-4775828 chr6:4776302-4776311
36	JUND	chr6:4775730-4776193	A549	lung:	n/a	n/a
37	POLR2A	chr6:4775605-4777703	GM19193	blood:	n/a	n/a
38	MAZ	chr6:4775495-4776996	HepG2	liver:	n/a	chr6:4775819-4775828 chr6:4776302-4776311
39	RAD21	chr6:4775798-4776398	H1-hESC	embryonic stem cell:	n/a	chr6:4775990-4776004
40	JUND	chr6:4775662-4776861	A549	lung:	n/a	chr6:4776558-4776572
41	RAD21	chr6:4775736-4776954	IMR90	lung:	n/a	chr6:4776490-4776502 chr6:4775990-4776004
42	TAF1	chr6:4775761-4777066	HepG2	liver:	n/a	n/a
43	YY1	chr6:4775684-4776332	GM12878	blood:	n/a	chr6:4775989-4775998 chr6:4776136-4776150 chr6:4775996-4776010 chr6:4775989-4776003
44	MYC	chr6:4775342-4776933	NB4	blood:	n/a	chr6:4775819-4775828 chr6:4776302-4776311
45	POLR2A	chr6:4775552-4775890	GM12878	blood:	n/a	n/a
46	SPI1	chr6:4775192-4775971	HL-60	blood:	n/a	chr6:4775492-4775505
47	POLR2A	chr6:4774822-4775895	PBDE	blood:	n/a	n/a
48	POLR2A	chr6:4775491-4775879	MCF-7	breast:	n/a	n/a
49	POLR2A	chr6:4774970-4776396	ECC-1	luminal epithelium:	n/a	n/a
50	MAX	chr6:4774991-4777114	HepG2	liver:	n/a	chr6:4775819-4775828 chr6:4776302-4776311

No.	Distal block	Cell Line	Cell type
1	chr6:4775417..4779410-chr6:4834974..4837006,3	MCF-7	breast:
2	chr6:4775727..4780301-chr6:4925378..4930668,5	K562	blood:
3	chr6:4775660..4776622-chr6:5030960..5031503,2	MCF-7	breast:

Variant related genes	Relation type
CDYL	TF binding region
ENSG00000236336	TF binding region
ENSG00000153046	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	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3429586	chr6:4719363-4792438	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv3358796	chr6:4775353-4778326	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3405553	chr6:4775578-4778126	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3438069	chr6:4775703-4778001	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4772600-4776200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:4772800-4777200	Active TSS	H1 Cell Line	embryonic stem cell
3	chr6:4772800-4777800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:4773000-4777400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:4773000-4777600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:4773200-4777400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr6:4773200-4777400	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr6:4773200-4777400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:4773200-4777600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:4773200-4778200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:4774200-4778000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:4774600-4777400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr6:4774800-4777800	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr6:4774800-4778000	Active TSS	Stomach Smooth Muscle	stomach
15	chr6:4775000-4777000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:4775000-4777000	Active TSS	Placenta Amnion	Placenta Amnion
17	chr6:4775000-4777600	Active TSS	Brain Substantia Nigra	brain
18	chr6:4775000-4777800	Active TSS	Brain Angular Gyrus	brain
19	chr6:4775000-4777800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:4775000-4777800	Active TSS	Colon Smooth Muscle	Colon
21	chr6:4775000-4777800	Active TSS	Esophagus	oesophagus
22	chr6:4775000-4777800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr6:4775000-4777800	Active TSS	Gastric	stomach
24	chr6:4775000-4777800	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr6:4775000-4777800	Active TSS	Rectal Smooth Muscle	rectum
26	chr6:4775000-4778000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:4775000-4778000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:4775000-4778000	Active TSS	Ovary	ovary
29	chr6:4775000-4778400	Active TSS	Brain Cingulate Gyrus	brain
30	chr6:4775000-4778400	Active TSS	A549	lung
31	chr6:4775200-4776200	Bivalent/Poised TSS	Fetal Brain Female	brain
32	chr6:4775200-4776200	Bivalent/Poised TSS	Thymus	Thymus
33	chr6:4775200-4776400	Active TSS	Fetal Kidney	kidney
34	chr6:4775200-4777600	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr6:4775200-4777600	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr6:4775200-4777600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:4775200-4777800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:4775200-4777800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:4775200-4778000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:4775200-4778000	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr6:4775200-4778000	Active TSS	Psoas Muscle	Psoas
42	chr6:4775200-4778400	Active TSS	Aorta	Aorta
43	chr6:4775400-4777800	Active TSS	Brain Hippocampus Middle	brain
44	chr6:4775400-4777800	Active TSS	Lung	lung
45	chr6:4775400-4777800	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr6:4775400-4778000	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr6:4775400-4778000	Active TSS	Small Intestine	intestine
48	chr6:4775600-4776200	Transcr. at gene 5' and 3'	Right Atrium	heart
49	chr6:4775600-4776400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
50	chr6:4775600-4776400	Bivalent/Poised TSS	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links