Variant report

Variant	rs548498605
Chromosome Location	chr6:12009359-12009360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:301)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:301 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr6:12009037-12009537	PANC-1	pancreas:	n/a	n/a
2	PAX5	chr6:12008554-12009457	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:12009005-12009525	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr6:12009122-12009394	HepG2	liver:	n/a	n/a
5	ZMIZ1	chr6:12008264-12009836	K562	blood:	n/a	n/a
6	TEAD4	chr6:12008221-12009775	K562	blood:	n/a	n/a
7	BHLHE40	chr6:12008368-12009828	GM12878	blood:	n/a	chr6:12009310-12009326
8	MAX	chr6:12008711-12009572	A549	lung:	n/a	chr6:12009161-12009170
9	MAX	chr6:12008484-12009867	Hela-S3	cervix:	n/a	chr6:12009161-12009170
10	MAX	chr6:12008442-12009754	A549	lung:	n/a	chr6:12009161-12009170
11	ELF1	chr6:12008504-12009412	GM12878	blood:	n/a	chr6:12009309-12009321 chr6:12009261-12009273 chr6:12009268-12009280
12	TCF12	chr6:12008658-12009386	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:12009026-12009521	Gliobla	brain:	n/a	n/a
14	POLR2A	chr6:12008400-12011637	K562	blood:	n/a	n/a
15	HCFC1	chr6:12008484-12009740	K562	blood:	n/a	n/a
16	POLR2A	chr6:12008545-12013822	GM18951	blood:	n/a	n/a
17	TRIM28	chr6:12008373-12009400	K562	blood:	n/a	n/a
18	POLR2A	chr6:12008481-12009757	GM18526	blood:	n/a	n/a
19	POLR2A	chr6:12008516-12013922	GM19193	blood:	n/a	n/a
20	PAX5	chr6:12009088-12009626	GM12892	blood:	n/a	n/a
21	MAX	chr6:12008501-12009865	K562	blood:	n/a	chr6:12009161-12009170
22	MXI1	chr6:12008646-12009889	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:12008529-12009874	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:12007817-12015834	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:12008475-12009815	Hela-S3	cervix:	n/a	n/a
26	ETS1	chr6:12008639-12009382	GM12878	blood:	n/a	n/a
27	JUND	chr6:12009008-12009415	A549	lung:	n/a	n/a
28	TAF1	chr6:12008489-12009814	GM12878	blood:	n/a	n/a
29	CCNT2	chr6:12008406-12009802	K562	blood:	n/a	n/a
30	POLR2A	chr6:12008972-12009376	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr6:12008727-12009407	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr6:12009093-12009535	A549	lung:	n/a	n/a
33	POLR2A	chr6:12008496-12009441	HCT-116	colon:	n/a	n/a
34	POLR2A	chr6:12008458-12009369	SK-N-SH	brain:	n/a	n/a
35	FOXM1	chr6:12008506-12009378	GM12878	blood:	n/a	n/a
36	TCF12	chr6:12008535-12009612	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr6:12007783-12012797	K562	blood:	n/a	n/a
38	EGR1	chr6:12008713-12009583	GM12878	blood:	n/a	n/a
39	TEAD4	chr6:12008773-12009785	SK-N-SH	brain:	n/a	n/a
40	PAX5	chr6:12009072-12009365	GM12878	blood:	n/a	n/a
41	POLR2A	chr6:12008239-12015396	IMR90	lung:	n/a	n/a
42	POLR2A	chr6:12009042-12009367	A549	lung:	n/a	n/a
43	EP300	chr6:12009096-12009516	T-47D	breast:	n/a	chr6:12009312-12009321 chr6:12009255-12009271
44	EBF1	chr6:12008766-12009881	GM12878	blood:	n/a	chr6:12009624-12009635
45	EP300	chr6:12008673-12009542	T-47D	breast:	n/a	chr6:12009312-12009321 chr6:12009255-12009271
46	TAF1	chr6:12008632-12009654	HepG2	liver:	n/a	n/a
47	NFIC	chr6:12008762-12009428	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr6:12008763-12009404	HUVEC	blood vessel:	n/a	n/a
49	EP300	chr6:12008700-12009405	SK-N-SH_RA	brain:	n/a	chr6:12009312-12009321 chr6:12009255-12009271
50	CHD2	chr6:12008467-12009691	Hela-S3	cervix:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46237768..46238593-chr6:12009330..12009875,2	Hela-S3	cervix:
2	chr16:4475034..4475714-chr6:12008711..12009473,2	Hela-S3	cervix:
3	chr6:11873602..11875677-chr6:12009027..12011838,2	K562	blood:
4	chr6:11990947..11994181-chr6:12007149..12010077,3	K562	blood:
5	chr6:11804488..11807450-chr6:12008603..12011488,3	MCF-7	breast:
6	chr6:11935076..11937337-chr6:12009000..12010923,2	K562	blood:
7	chr6:11766846..11771135-chr6:12008831..12011747,3	K562	blood:
8	chr6:11865768..11868889-chr6:12009325..12011874,3	K562	blood:
9	chr6:12008844..12009838-chr7:134854735..134855590,2	Hela-S3	cervix:
10	chr11:71791436..71791948-chr6:12009007..12009560,2	Hela-S3	cervix:
11	chr6:12009134..12010743-chr6:12145646..12148619,2	MCF-7	breast:
12	chr6:11865768..11869319-chr6:12009325..12011874,4	K562	blood:
13	chr6:12009262..12013340-chr6:12286174..12290698,6	MCF-7	breast:
14	chr11:66383680..66384551-chr6:12008610..12009525,2	Hela-S3	cervix:
15	chr6:12008600..12009379-chr6:43737966..43738894,2	Hela-S3	cervix:
16	chr6:11733150..11736062-chr6:12007778..12010289,2	K562	blood:
17	chr6:11922704..11924727-chr6:12009251..12011603,2	K562	blood:

No data

Variant related genes	Relation type
HIVEP1	TF binding region
ENSG00000239306	Chromatin interaction
ENSG00000184900	Chromatin interaction
ENSG00000137497	Chromatin interaction
ENSG00000262246	Chromatin interaction
ENSG00000111863	Chromatin interaction
ENSG00000184154	Chromatin interaction
ENSG00000272114	Chromatin interaction
ENSG00000112715	Chromatin interaction
ENSG00000078401	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000122783	Chromatin interaction
ENSG00000225102	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv970323	chr6:12006884-12020375	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv10446	chr6:12008060-12013799	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv12680	chr6:12009115-12009764	Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12007400-12013400	Active TSS	K562	blood
2	chr6:12007800-12009800	Active TSS	Liver	Liver
3	chr6:12007800-12009800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr6:12007800-12009800	Bivalent/Poised TSS	HepG2	liver
5	chr6:12007800-12011400	Active TSS	Fetal Muscle Trunk	muscle
6	chr6:12008000-12014000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr6:12008200-12009800	Active TSS	Fetal Intestine Large	intestine
8	chr6:12008200-12010200	Active TSS	A549	lung
9	chr6:12008200-12010600	Active TSS	Fetal Muscle Leg	muscle
10	chr6:12008200-12014000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:12008400-12009600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:12008400-12009600	Active TSS	Brain Cingulate Gyrus	brain
13	chr6:12008400-12009600	Active TSS	Left Ventricle	heart
14	chr6:12008400-12009800	Active TSS	Pancreas	Pancrea
15	chr6:12008400-12010000	Active TSS	Brain Anterior Caudate	brain
16	chr6:12008400-12010000	Active TSS	Stomach Smooth Muscle	stomach
17	chr6:12008400-12010000	Active TSS	HSMMtube	muscle
18	chr6:12008400-12010800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:12008400-12010800	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr6:12008400-12011400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr6:12008400-12011600	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr6:12008400-12013600	Active TSS	Psoas Muscle	Psoas
23	chr6:12008400-12013800	Active TSS	Right Ventricle	heart
24	chr6:12008400-12014200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:12008600-12009600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:12008600-12009600	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr6:12008600-12009600	Active TSS	Fetal Heart	heart
28	chr6:12008600-12009800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:12008600-12009800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:12008600-12009800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:12008600-12009800	Active TSS	Brain Substantia Nigra	brain
32	chr6:12008600-12009800	Active TSS	Esophagus	oesophagus
33	chr6:12008600-12009800	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr6:12008600-12009800	Active TSS	Gastric	stomach
35	chr6:12008600-12009800	Active TSS	Ovary	ovary
36	chr6:12008600-12009800	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr6:12008600-12009800	Active TSS	Stomach Mucosa	stomach
38	chr6:12008600-12009800	Active TSS	Spleen	Spleen
39	chr6:12008600-12010000	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr6:12008600-12010000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:12008600-12010200	Active TSS	Brain Angular Gyrus	brain
42	chr6:12008600-12011400	Active TSS	Placenta Amnion	Placenta Amnion
43	chr6:12008600-12011800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr6:12008600-12014000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:12008600-12014000	Active TSS	Colonic Mucosa	Colon
46	chr6:12008600-12014200	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr6:12008600-12014400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:12008600-12014400	Active TSS	Aorta	Aorta
49	chr6:12008800-12009400	Active TSS	Primary hematopoietic stem cells	blood
50	chr6:12008800-12009600	Active TSS	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links