Variant report

Variant	rs7674353
Chromosome Location	chr4:47533838-47533839
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	POLR2A	chr4:47533789-47533929	HUVEC	blood vessel:	n/a	n/a
2	PAX5	chr4:47533611-47534115	GM12878	blood:	n/a	chr4:47533714-47533723
3	FOS	chr4:47533302-47534147	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr4:47533701-47534158	HL-60	blood:	n/a	n/a
5	YY1	chr4:47533626-47533998	GM12892	blood:	n/a	chr4:47533773-47533783
6	FOXM1	chr4:47533604-47534165	GM12878	blood:	n/a	n/a
7	FOS	chr4:47533320-47534007	MCF10A-Er-Src	breast:	n/a	n/a
8	NFIC	chr4:47533559-47534248	GM12878	blood:	n/a	n/a
9	IKZF1	chr4:47533674-47534059	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:47533711-47533965	ProgFib	skin:	n/a	n/a
11	MEF2A	chr4:47533639-47534180	GM12878	blood:	n/a	chr4:47533713-47533721
12	PML	chr4:47533719-47533961	GM12878	blood:	n/a	n/a
13	ATF2	chr4:47533593-47534069	GM12878	blood:	n/a	n/a
14	NFIC	chr4:47533487-47534255	GM12878	blood:	n/a	n/a
15	POLR2A	chr4:47533661-47534307	IMR90	lung:	n/a	n/a
16	MYC	chr4:47533758-47533995	MCF10A-Er-Src	breast:	n/a	n/a
17	EP300	chr4:47533705-47534290	GM12878	blood:	n/a	n/a
18	RUNX3	chr4:47533472-47534266	GM12878	blood:	n/a	chr4:47533893-47533910
19	STAT1	chr4:47533768-47533976	GM12878	blood:	n/a	n/a
20	EBF1	chr4:47533722-47534296	GM12878	blood:	n/a	n/a
21	CTCF	chr4:47533820-47533970	AG10803	skin:	n/a	n/a
22	GATA2	chr4:47533302-47534136	HUVEC	blood vessel:	n/a	chr4:47533713-47533723
23	GATA3	chr4:47532792-47534102	SK-N-SH	brain:	n/a	chr4:47533713-47533723
24	CHD1	chr4:47533633-47534067	GM12878	blood:	n/a	n/a
25	FOXM1	chr4:47533555-47534239	GM12878	blood:	n/a	n/a
26	BCLAF1	chr4:47533624-47534189	GM12878	blood:	n/a	n/a
27	EBF1	chr4:47533724-47534012	GM12878	blood:	n/a	n/a
28	TCF12	chr4:47533663-47533972	GM12878	blood:	n/a	n/a
29	PAX5	chr4:47533689-47533955	GM12878	blood:	n/a	chr4:47533714-47533723
30	SPI1	chr4:47533738-47534018	GM12878	blood:	n/a	n/a
31	YY1	chr4:47533641-47533948	GM12891	blood:	n/a	chr4:47533773-47533783
32	MAX	chr4:47533642-47534067	NB4	blood:	n/a	n/a
33	RUNX3	chr4:47533595-47534166	GM12878	blood:	n/a	chr4:47533893-47533910
34	BCL11A	chr4:47533703-47533967	GM12878	blood:	n/a	n/a
35	FOSL2	chr4:47533191-47534031	SK-N-SH	brain:	n/a	n/a
36	YY1	chr4:47533613-47533987	GM12878	blood:	n/a	chr4:47533773-47533783
37	YY1	chr4:47533647-47533981	GM12878	blood:	n/a	chr4:47533773-47533783
38	CHD2	chr4:47533656-47534084	GM12878	blood:	n/a	n/a
39	POLR2A	chr4:47533473-47534883	K562	blood:	n/a	n/a
40	SPI1	chr4:47533740-47534067	GM12891	blood:	n/a	n/a
41	POLR2A	chr4:47533292-47534252	HUVEC	blood vessel:	n/a	n/a
42	FOS	chr4:47533310-47534021	MCF10A-Er-Src	breast:	n/a	n/a
43	FOS	chr4:47533757-47533962	MCF10A-Er-Src	breast:	n/a	n/a
44	TCF12	chr4:47533641-47534027	GM12878	blood:	n/a	chr4:47533646-47533656
45	MYC	chr4:47533692-47533957	MCF10A-Er-Src	breast:	n/a	n/a
46	TCF3	chr4:47533640-47534044	GM12878	blood:	n/a	n/a
47	RCOR1	chr4:47532314-47534358	IMR90	lung:	n/a	n/a
48	MYC	chr4:47533667-47534064	NB4	blood:	n/a	n/a
49	POLR2A	chr4:47533623-47534167	HL-60	blood:	n/a	n/a
50	STAT3	chr4:47533821-47533958	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:47523458..47525968-chr4:47532454..47534503,2	K562	blood:
2	chr4:47533452..47535756-chr4:47565106..47567780,2	K562	blood:

Variant related genes	Relation type
ATP10D	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10004038	1.00[CHB][hapmap]
rs10021442	1.00[CHB][hapmap]
rs10027156	1.00[ASN][1000 genomes]
rs11932436	1.00[CHB][hapmap]
rs11941639	1.00[CHB][hapmap]
rs11947712	1.00[CHB][hapmap]
rs1316783	1.00[CHB][hapmap]
rs13435606	1.00[CHB][hapmap]
rs16860404	1.00[CHB][hapmap]
rs17462783	1.00[CHB][hapmap]
rs17572227	1.00[CHB][hapmap]
rs17572234	1.00[CHB][hapmap]
rs17572617	1.00[CHB][hapmap]
rs28647985	1.00[ASN][1000 genomes]
rs4362797	0.86[ASN][1000 genomes]
rs4423850	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4467534	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4467535	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4475121	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4599383	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4694851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695239	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695243	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6447564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835978	1.00[CHB][hapmap]
rs6837171	0.86[ASN][1000 genomes]
rs6837743	1.00[ASN][1000 genomes]
rs6842769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6849863	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857999	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs73237050	1.00[ASN][1000 genomes]
rs73237070	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237074	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237078	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237080	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237081	1.00[ASN][1000 genomes]
rs73237082	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237083	1.00[ASN][1000 genomes]
rs73237084	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237085	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237086	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237087	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237088	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237089	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237090	1.00[ASN][1000 genomes]
rs73237091	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999398	1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879005	chr4:47408838-47548254	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv829923	chr4:47436139-47678443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv997471	chr4:47489412-47895223	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv998892	chr4:47493552-47863354	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv537081	chr4:47493552-47863354	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv528326	chr4:47525054-47533838	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv879006	chr4:47525054-47555196	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47488800-47559800	Weak transcription	Right Ventricle	heart
2	chr4:47512200-47536800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:47512400-47577200	Weak transcription	Small Intestine	intestine
4	chr4:47513800-47534000	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:47514000-47551000	Weak transcription	Gastric	stomach
6	chr4:47516000-47534000	Weak transcription	Stomach Mucosa	stomach
7	chr4:47516400-47547800	Weak transcription	Ovary	ovary
8	chr4:47516400-47548200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:47518000-47544800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:47525200-47540600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:47525200-47544000	Weak transcription	Fetal Intestine Small	intestine
12	chr4:47526200-47534000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:47526400-47559800	Weak transcription	Pancreas	Pancrea
14	chr4:47528000-47538400	Weak transcription	Adipose Nuclei	Adipose
15	chr4:47530200-47536400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:47530400-47536600	Enhancers	HMEC	breast
17	chr4:47531000-47536000	Weak transcription	Liver	Liver
18	chr4:47531600-47536200	Weak transcription	Fetal Kidney	kidney
19	chr4:47531600-47536800	Weak transcription	Fetal Lung	lung
20	chr4:47531600-47537000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:47531800-47537800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:47532000-47537200	Weak transcription	Fetal Intestine Large	intestine
23	chr4:47532200-47534600	Enhancers	Placenta Amnion	Placenta Amnion
24	chr4:47532200-47536000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:47532200-47536000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:47532200-47536400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:47532200-47536600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:47532200-47550400	Weak transcription	Fetal Muscle Leg	muscle
29	chr4:47532400-47534400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:47532400-47534600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:47532600-47534000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr4:47532600-47534000	Enhancers	NHDF-Ad	bronchial
33	chr4:47532600-47534600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:47532600-47534800	Enhancers	NHLF	lung
35	chr4:47532600-47536600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr4:47532600-47536600	Enhancers	HUVEC	blood vessel
37	chr4:47532800-47534400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:47532800-47535000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:47532800-47536200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:47532800-47536400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:47532800-47536600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:47532800-47536600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr4:47533000-47534000	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr4:47533000-47534000	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr4:47533000-47534000	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr4:47533000-47534000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:47533000-47534200	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr4:47533000-47534400	Enhancers	Colon Smooth Muscle	Colon
49	chr4:47533000-47534400	Enhancers	Placenta	Placenta
50	chr4:47533000-47534400	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links