Variant report

Variant	rs9999398
Chromosome Location	chr4:47533601-47533602
allele	A/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	FOXA1	chr4:47533287-47533719	T-47D	breast:	n/a	n/a
2	FOS	chr4:47533302-47534147	HUVEC	blood vessel:	n/a	n/a
3	FOS	chr4:47533320-47534007	MCF10A-Er-Src	breast:	n/a	n/a
4	NFIC	chr4:47533559-47534248	GM12878	blood:	n/a	n/a
5	ATF2	chr4:47533593-47534069	GM12878	blood:	n/a	n/a
6	YY1	chr4:47533244-47533694	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr4:47533280-47533645	SK-N-SH	brain:	n/a	n/a
8	NFIC	chr4:47533487-47534255	GM12878	blood:	n/a	n/a
9	RUNX3	chr4:47533472-47534266	GM12878	blood:	n/a	chr4:47533893-47533910
10	GATA2	chr4:47533302-47534136	HUVEC	blood vessel:	n/a	chr4:47533713-47533723
11	GATA3	chr4:47532792-47534102	SK-N-SH	brain:	n/a	chr4:47533713-47533723
12	FOXM1	chr4:47533555-47534239	GM12878	blood:	n/a	n/a
13	CEBPB	chr4:47533306-47533630	Hela-S3	cervix:	n/a	n/a
14	RUNX3	chr4:47533595-47534166	GM12878	blood:	n/a	chr4:47533893-47533910
15	FOSL2	chr4:47533191-47534031	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr4:47533473-47534883	K562	blood:	n/a	n/a
17	POLR2A	chr4:47533292-47534252	HUVEC	blood vessel:	n/a	n/a
18	FOS	chr4:47533310-47534021	MCF10A-Er-Src	breast:	n/a	n/a
19	EP300	chr4:47533332-47533761	ECC-1	luminal epithelium:	n/a	n/a
20	TEAD4	chr4:47533175-47533773	ECC-1	luminal epithelium:	n/a	n/a
21	RCOR1	chr4:47532314-47534358	IMR90	lung:	n/a	n/a
22	EP300	chr4:47533594-47534040	GM12878	blood:	n/a	n/a
23	GATA3	chr4:47532708-47534152	SK-N-SH	brain:	n/a	chr4:47533713-47533723
24	CEBPB	chr4:47533357-47534135	IMR90	lung:	n/a	n/a
25	TEAD4	chr4:47533188-47533734	ECC-1	luminal epithelium:	n/a	n/a
26	YY1	chr4:47533600-47533918	GM12892	blood:	n/a	chr4:47533773-47533783
27	TEAD4	chr4:47533219-47533696	H1-hESC	embryonic stem cell:	n/a	n/a
28	CHD1	chr4:47533181-47534326	IMR90	lung:	n/a	n/a
29	TEAD4	chr4:47533181-47533748	H1-hESC	embryonic stem cell:	n/a	n/a
30	ATF2	chr4:47533555-47534185	GM12878	blood:	n/a	n/a
31	MTA3	chr4:47533516-47534227	GM12878	blood:	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: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10027156	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28647985	1.00[ASN][1000 genomes]
rs4132384	0.96[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs4362797	0.86[ASN][1000 genomes]
rs4423850	1.00[ASN][1000 genomes]
rs4467534	1.00[ASN][1000 genomes]
rs4467535	1.00[ASN][1000 genomes]
rs4475121	1.00[ASN][1000 genomes]
rs4599383	0.86[ASN][1000 genomes]
rs4694851	1.00[ASN][1000 genomes]
rs4695239	1.00[ASN][1000 genomes]
rs4695243	0.89[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447564	1.00[ASN][1000 genomes]
rs6837171	0.86[ASN][1000 genomes]
rs6837743	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6842769	1.00[ASN][1000 genomes]
rs6849863	1.00[ASN][1000 genomes]
rs73237050	1.00[ASN][1000 genomes]
rs73237070	1.00[ASN][1000 genomes]
rs73237074	1.00[ASN][1000 genomes]
rs73237078	1.00[ASN][1000 genomes]
rs73237080	1.00[ASN][1000 genomes]
rs73237081	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237082	1.00[ASN][1000 genomes]
rs73237083	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237084	1.00[ASN][1000 genomes]
rs73237085	1.00[ASN][1000 genomes]
rs73237086	1.00[ASN][1000 genomes]
rs73237087	1.00[ASN][1000 genomes]
rs73237088	1.00[ASN][1000 genomes]
rs73237089	1.00[ASN][1000 genomes]
rs73237090	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237091	1.00[ASN][1000 genomes]
rs7662844	0.96[EUR][1000 genomes]
rs7674353	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7675970	0.95[EUR][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:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47488000-47533800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:47488800-47559800	Weak transcription	Right Ventricle	heart
3	chr4:47512200-47536800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:47512400-47577200	Weak transcription	Small Intestine	intestine
5	chr4:47513800-47534000	Weak transcription	Brain Hippocampus Middle	brain
6	chr4:47514000-47551000	Weak transcription	Gastric	stomach
7	chr4:47514200-47533800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:47515800-47533800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:47515800-47533800	Weak transcription	Lung	lung
10	chr4:47516000-47534000	Weak transcription	Stomach Mucosa	stomach
11	chr4:47516400-47547800	Weak transcription	Ovary	ovary
12	chr4:47516400-47548200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:47518000-47544800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:47525200-47533800	Weak transcription	Fetal Stomach	stomach
15	chr4:47525200-47540600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:47525200-47544000	Weak transcription	Fetal Intestine Small	intestine
17	chr4:47526200-47534000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:47526400-47559800	Weak transcription	Pancreas	Pancrea
19	chr4:47526600-47533800	Weak transcription	Left Ventricle	heart
20	chr4:47528000-47538400	Weak transcription	Adipose Nuclei	Adipose
21	chr4:47530200-47536400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:47530400-47536600	Enhancers	HMEC	breast
23	chr4:47531000-47536000	Weak transcription	Liver	Liver
24	chr4:47531600-47536200	Weak transcription	Fetal Kidney	kidney
25	chr4:47531600-47536800	Weak transcription	Fetal Lung	lung
26	chr4:47531600-47537000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:47531800-47537800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr4:47532000-47537200	Weak transcription	Fetal Intestine Large	intestine
29	chr4:47532200-47534600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr4:47532200-47536000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:47532200-47536000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:47532200-47536400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:47532200-47536600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:47532200-47550400	Weak transcription	Fetal Muscle Leg	muscle
35	chr4:47532400-47534400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:47532400-47534600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:47532600-47533800	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr4:47532600-47534000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr4:47532600-47534000	Enhancers	NHDF-Ad	bronchial
40	chr4:47532600-47534600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:47532600-47534800	Enhancers	NHLF	lung
42	chr4:47532600-47536600	Enhancers	Primary T cells fromperipheralblood	blood
43	chr4:47532600-47536600	Enhancers	HUVEC	blood vessel
44	chr4:47532800-47533800	Enhancers	HSMM	muscle
45	chr4:47532800-47534400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:47532800-47535000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:47532800-47536200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:47532800-47536400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:47532800-47536600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:47532800-47536600	Enhancers	Primary T helper cells fromperipheralblood	blood

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