Variant report

Variant	rs377466405
Chromosome Location	chr6:49430801-49430802
allele	C/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	SP1	chr6:49430703-49431377	A549	lung:	n/a	chr6:49430754-49430768 chr6:49430908-49430917
2	MAX	chr6:49430767-49431347	SK-N-SH	brain:	n/a	n/a
3	GABPA	chr6:49430787-49431334	Hela-S3	cervix:	n/a	chr6:49431064-49431071
4	POLR2A	chr6:49430646-49431270	HepG2	liver:	n/a	n/a
5	ELF1	chr6:49430774-49431297	A549	lung:	n/a	chr6:49431082-49431093 chr6:49431082-49431093 chr6:49431083-49431092
6	GABPA	chr6:49430753-49431313	HepG2	liver:	n/a	chr6:49431064-49431071
7	RUNX3	chr6:49430659-49431345	GM12878	blood:	n/a	chr6:49430922-49430939
8	CREB1	chr6:49430563-49431533	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF12	chr6:49430702-49430886	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:49430346-49431460	GM12878	blood:	n/a	n/a
11	SRF	chr6:49430618-49431481	HCT-116	colon:	n/a	n/a
12	SREBP1	chr6:49430697-49431150	HepG2	liver:	n/a	n/a
13	ATF3	chr6:49430743-49431444	K562	blood:	n/a	n/a
14	MAZ	chr6:49430336-49431604	K562	blood:	n/a	n/a
15	ARID3A	chr6:49430669-49431330	HepG2	liver:	n/a	n/a
16	MYBL2	chr6:49430441-49431520	HepG2	liver:	n/a	n/a
17	E2F6	chr6:49430625-49431640	K562	blood:	n/a	chr6:49431112-49431123 chr6:49431109-49431126 chr6:49430905-49430917 chr6:49431109-49431126
18	ELF1	chr6:49430651-49431427	HCT-116	colon:	n/a	chr6:49431377-49431388 chr6:49431082-49431093 chr6:49431082-49431093 chr6:49431083-49431092
19	REST	chr6:49430779-49431387	A549	lung:	n/a	chr6:49430936-49430949
20	STAT3	chr6:49430678-49431249	GM12878	blood:	n/a	n/a
21	MAX	chr6:49430539-49431407	HCT-116	colon:	n/a	n/a
22	SIN3A	chr6:49430267-49432021	H1-hESC	embryonic stem cell:	n/a	n/a
23	EGR1	chr6:49430482-49431413	HCT-116	colon:	n/a	chr6:49430906-49430920 chr6:49431082-49431091 chr6:49430963-49430977
24	ELF1	chr6:49430673-49431586	HepG2	liver:	n/a	chr6:49431377-49431388 chr6:49431082-49431093 chr6:49431082-49431093 chr6:49431083-49431092
25	POLR2A	chr6:49430553-49431480	GM12892	blood:	n/a	n/a
26	MAX	chr6:49430755-49431336	SK-N-SH	brain:	n/a	n/a
27	EGR1	chr6:49430692-49431330	K562	blood:	n/a	chr6:49430906-49430920 chr6:49431082-49431091 chr6:49430963-49430977
28	MAX	chr6:49430727-49431523	K562	blood:	n/a	n/a
29	POLR2A	chr6:49430241-49431637	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr6:49430572-49431397	GM12892	blood:	n/a	n/a
31	RCOR1	chr6:49430496-49431255	HepG2	liver:	n/a	n/a
32	IRF1	chr6:49430592-49431382	K562	blood:	n/a	n/a
33	HEY1	chr6:49430505-49431732	K562	blood:	n/a	n/a
34	CTCF	chr6:49430800-49430950	GM06990	blood:	n/a	n/a
35	POLR2A	chr6:49430612-49431409	Raji	blood:	n/a	n/a
36	CREB1	chr6:49430633-49431323	H1-hESC	embryonic stem cell:	n/a	n/a
37	ELF1	chr6:49430684-49431298	GM12878	blood:	n/a	chr6:49431082-49431093 chr6:49431082-49431093 chr6:49431083-49431092
38	REST	chr6:49430106-49431541	H1-neurons	neurons:	n/a	chr6:49430936-49430949 chr6:49430509-49430529 chr6:49430515-49430529
39	CHD1	chr6:49430423-49431181	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:49430681-49431298	H1-hESC	embryonic stem cell:	n/a	n/a
41	TAF7	chr6:49430645-49431380	H1-hESC	embryonic stem cell:	n/a	n/a
42	GTF2F1	chr6:49430704-49431419	K562	blood:	n/a	n/a
43	E2F4	chr6:49430698-49431584	K562	blood:	n/a	chr6:49431113-49431124 chr6:49431112-49431123 chr6:49431109-49431126 chr6:49430905-49430917 chr6:49431109-49431126
44	TAF1	chr6:49430689-49431104	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:49430693-49431320	HUVEC	blood vessel:	n/a	n/a
46	HCFC1	chr6:49430429-49431502	K562	blood:	n/a	n/a
47	EGR1	chr6:49430667-49431334	ECC-1	luminal epithelium:	n/a	chr6:49430906-49430920 chr6:49431082-49431091 chr6:49430963-49430977
48	EGR1	chr6:49430764-49431298	ECC-1	luminal epithelium:	n/a	chr6:49430906-49430920 chr6:49431082-49431091 chr6:49430963-49430977
49	SIN3AK20	chr6:49430569-49431581	MCF-7	breast:	n/a	n/a
50	CTCF	chr6:49430800-49431090	GM12867	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:49430788-49430838	NT2-D1	testis:	n/a
2	chr6:49430788-49430838	HepG2	liver:	n/a
3	chr6:49430788-49430838	MCF-7	breast:	n/a
4	chr6:49430788-49430838	Caco-2	colon:	n/a
5	chr6:49430788-49430838	GM12892	blood:	n/a
6	chr6:49430788-49430838	NHDF-neo	bronchial:	n/a
7	chr6:49430788-49430838	AG10803	skin:	n/a
8	chr6:49430788-49430838	ProgFib	skin:	n/a
9	chr6:49430788-49430838	HCT-116	colon:	n/a
10	chr6:49430788-49430838	LNCaP	prostate:	n/a
11	chr6:49430788-49430838	HRE	kidney:	n/a
12	chr6:49430788-49430838	PFSK-1	brain:	n/a
13	chr6:49430788-49430838	HEEpiC	esophagus:	n/a
14	chr6:49430788-49430838	AG09309	skin:	n/a
15	chr6:49430788-49430838	PrEC	prostate:	n/a
16	chr6:49430788-49430838	ovcar-3	ovarian:	n/a
17	chr6:49430788-49430838	HL-60	blood:	n/a
18	chr6:49430788-49430838	HRCEpiC	kidney:	n/a
19	chr6:49430788-49430838	AG04449	skin:	fetal
20	chr6:49430788-49430838	BJ	skin:	n/a
21	chr6:49430788-49430838	NHBE	bronchial:	n/a
22	chr6:49430788-49430838	GM12891	blood:	n/a
23	chr6:49430788-49430838	HAEpiC	amniotic membrane:	n/a
24	chr6:49430788-49430838	A549	lung:	n/a
25	chr6:49430788-49430838	HEK293	kidney:	embryo
26	chr6:49430788-49430838	IMR90	lung:	fetal
27	chr6:49430788-49430838	GM19239	blood:	n/a
28	chr6:49430788-49430838	AoSMC	blood vessel:	n/a
29	chr6:49430788-49430838	U87	brain:	n/a
30	chr6:49430788-49430838	BE2_C	brain:	n/a
31	chr6:49430788-49430838	SAEC	small airway:	n/a
32	chr6:49430788-49430838	SK-N-MC	brain:	n/a
33	chr6:49430788-49430838	T-47D	breast:	n/a
34	chr6:49430788-49430838	Hepatocyte	liver:	n/a
35	chr6:49430788-49430838	MCF10A-Er-Src	breast:	n/a
36	chr6:49430788-49430838	RPTEC	kidney:	n/a
37	chr6:49430788-49430838	SK-N-SH	brain:	n/a
38	chr6:49430788-49430838	HCM	heart:	n/a
39	chr6:49430788-49430838	SK-N-SH_RA	brain:	n/a
40	chr6:49430788-49430838	GM12878	blood:	n/a
41	chr6:49430788-49430838	ECC-1	luminal epithelium:	n/a
42	chr6:49430788-49430838	HCPEpiC	choroid plexus:	n/a
43	chr6:49430788-49430838	HCF	heart:	n/a
44	chr6:49430788-49430838	AG04450	lung:	fetal
45	chr6:49430788-49430838	AG09319	gingival:	n/a
46	chr6:49430788-49430838	NH-A	brain:	n/a
47	chr6:49430788-49430838	CMK	blood:	n/a
48	chr6:49430788-49430838	HMEC	breast:	n/a
49	chr6:49430788-49430838	HIPEpiC	eye:	n/a
50	chr6:49430788-49430838	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:65596663..65597464-chr6:49430249..49430946,2	Hela-S3	cervix:
2	chr6:49429949..49432434-chr6:49603239..49605832,3	K562	blood:
3	chr6:20401677..20404627-chr6:49430582..49432502,2	K562	blood:
4	chr12:53845489..53846145-chr6:49430663..49431569,2	Hela-S3	cervix:
5	chr6:49419838..49421598-chr6:49428414..49430900,2	K562	blood:
6	chr6:49428075..49430840-chr6:49629508..49632761,3	K562	blood:
7	chr6:49429390..49432411-chr6:49516710..49519961,3	MCF-7	breast:
8	chr6:49428409..49430841-chr6:49452599..49454961,2	K562	blood:
9	chr17:76124180..76124774-chr6:49430693..49431317,2	Hela-S3	cervix:

Variant related genes	Relation type
CENPQ	TF binding region
CENPQ	CpG island
ENSG00000197261	Chromatin interaction
ENSG00000112242	Chromatin interaction
ENSG00000112077	Chromatin interaction
ENSG00000141524	Chromatin interaction
ENSG00000197111	Chromatin interaction
ENSG00000200156	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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv603081	chr6:49421241-49446233	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv603082	chr6:49421241-49446509	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv603083	chr6:49429706-49446233	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv603084	chr6:49429706-49446509	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv603085	chr6:49429706-49450341	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49429000-49434200	Active TSS	GM12878-XiMat	blood
2	chr6:49429200-49432000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:49429400-49432000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:49429400-49432000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:49429400-49432200	Active TSS	Ovary	ovary
6	chr6:49429400-49432200	Active TSS	Right Atrium	heart
7	chr6:49429600-49431600	Active TSS	Brain Cingulate Gyrus	brain
8	chr6:49429600-49431600	Active TSS	Brain Substantia Nigra	brain
9	chr6:49429600-49431600	Active TSS	Stomach Smooth Muscle	stomach
10	chr6:49429600-49431800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:49429600-49431800	Active TSS	Psoas Muscle	Psoas
12	chr6:49429600-49431800	Active TSS	Right Ventricle	heart
13	chr6:49429600-49432000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:49429600-49432000	Active TSS	Colonic Mucosa	Colon
15	chr6:49429600-49432000	Active TSS	NHDF-Ad	bronchial
16	chr6:49429600-49432200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr6:49429600-49432200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:49429600-49432200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr6:49429600-49432200	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr6:49429600-49432200	Active TSS	Fetal Kidney	kidney
21	chr6:49429600-49432200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr6:49429600-49432200	Active TSS	NHLF	lung
23	chr6:49429800-49431400	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr6:49429800-49431600	Active TSS	Aorta	Aorta
25	chr6:49429800-49431800	Active TSS	Left Ventricle	heart
26	chr6:49429800-49432000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:49429800-49432000	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr6:49429800-49432000	Active TSS	HSMMtube	muscle
29	chr6:49429800-49432400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:49430000-49431200	Active TSS	Thymus	Thymus
31	chr6:49430000-49431400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr6:49430000-49431400	Active TSS	Fetal Muscle Leg	muscle
33	chr6:49430000-49431400	Active TSS	Fetal Stomach	stomach
34	chr6:49430000-49431600	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr6:49430000-49431600	Active TSS	Fetal Intestine Small	intestine
36	chr6:49430000-49431600	Active TSS	Rectal Smooth Muscle	rectum
37	chr6:49430000-49431800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:49430000-49431800	Active TSS	Fetal Intestine Large	intestine
39	chr6:49430000-49432000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:49430000-49432000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:49430000-49432000	Active TSS	Fetal Muscle Trunk	muscle
42	chr6:49430000-49432000	Active TSS	Fetal Thymus	thymus
43	chr6:49430000-49432200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:49430000-49432200	Active TSS	Fetal Lung	lung
45	chr6:49430000-49432200	Active TSS	A549	lung
46	chr6:49430000-49432400	Active TSS	K562	blood
47	chr6:49430000-49432600	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr6:49430000-49432600	Active TSS	Muscle Satellite Cultured Cells	--
49	chr6:49430200-49431400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:49430200-49431600	ZNF genes & repeats	Fetal Brain Male	brain

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