Variant report

Variant	rs17728804
Chromosome Location	chr4:56751099-56751100
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	GATA3	chr4:56750974-56751368	SH-SY5Y	brain:	n/a	chr4:56751152-56751168 chr4:56751152-56751168 chr4:56751150-56751171 chr4:56751155-56751165
2	MAFF	chr4:56750928-56751372	K562	blood:	n/a	n/a
3	RCOR1	chr4:56751045-56751245	K562	blood:	n/a	n/a
4	IRF1	chr4:56750742-56751308	K562	blood:	n/a	n/a
5	JUND	chr4:56751086-56751286	K562	blood:	n/a	n/a
6	EP300	chr4:56751034-56751392	K562	blood:	n/a	n/a
7	MAFK	chr4:56751004-56751365	K562	blood:	n/a	chr4:56751193-56751213

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56749468..56751302-chr4:56754110..56755765,2	K562	blood:

Variant related genes	Relation type
EXOC1	TF binding region
RNU6-652P	TF binding region
ENSG00000090989	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1072799	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727702	0.89[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729456	0.90[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734942	0.90[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086132	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086150	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086186	1.00[ASN][1000 genomes]
rs17086254	1.00[ASN][1000 genomes]
rs17740755	1.00[ASN][1000 genomes]
rs17742000	1.00[ASN][1000 genomes]
rs17742722	1.00[ASN][1000 genomes]
rs17743071	1.00[ASN][1000 genomes]
rs17797113	1.00[ASN][1000 genomes]
rs17797407	1.00[ASN][1000 genomes]
rs17797571	1.00[ASN][1000 genomes]
rs17797595	1.00[ASN][1000 genomes]
rs17798452	1.00[ASN][1000 genomes]
rs17798872	1.00[ASN][1000 genomes]
rs2899046	1.00[ASN][1000 genomes]
rs2899053	1.00[ASN][1000 genomes]
rs34179097	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34184679	1.00[ASN][1000 genomes]
rs35143702	1.00[ASN][1000 genomes]
rs41279543	1.00[ASN][1000 genomes]
rs41280345	1.00[ASN][1000 genomes]
rs56026480	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61753870	1.00[ASN][1000 genomes]
rs6814812	0.89[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817717	0.90[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833480	1.00[ASN][1000 genomes]
rs6845953	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848009	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238359	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238365	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238367	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238368	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238369	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238370	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238371	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238372	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238373	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238377	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238379	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238380	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238381	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238382	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238383	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238384	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238387	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238390	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238395	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238397	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238398	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238399	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238400	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748013	0.90[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657912	0.90[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669903	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675287	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675490	0.86[EUR][1000 genomes]
rs7690739	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698100	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9994601	1.00[ASN][1000 genomes]

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	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3406311	chr4:56580578-56840877	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv427681	chr4:56651921-56908209	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv879024	chr4:56742205-56786589	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv879025	chr4:56742205-56808607	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56720400-56764600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:56720800-56761800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:56721600-56774600	Weak transcription	Fetal Heart	heart
4	chr4:56724400-56752400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:56732600-56754000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:56733200-56763000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:56733600-56763000	Weak transcription	Stomach Mucosa	stomach
8	chr4:56733800-56772200	Weak transcription	Hela-S3	cervix
9	chr4:56733800-56772800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr4:56734400-56751200	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr4:56734400-56773000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr4:56734600-56753400	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:56734600-56773400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:56735000-56768000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:56736000-56762400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:56737000-56774800	Weak transcription	Psoas Muscle	Psoas
17	chr4:56737600-56763400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:56738000-56771400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:56739800-56759800	Weak transcription	HMEC	breast
20	chr4:56742800-56751800	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr4:56743400-56751400	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:56743400-56752000	Strong transcription	Placenta	Placenta
23	chr4:56743600-56751800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr4:56743600-56752600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:56743600-56752600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr4:56743800-56752800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:56745600-56760000	Weak transcription	Fetal Kidney	kidney
28	chr4:56745800-56757400	Weak transcription	Brain Substantia Nigra	brain
29	chr4:56745800-56757800	Weak transcription	Brain Germinal Matrix	brain
30	chr4:56745800-56759800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:56745800-56772800	Weak transcription	Small Intestine	intestine
32	chr4:56747200-56752200	Strong transcription	Osteobl	bone
33	chr4:56747400-56758800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr4:56747600-56756200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:56747800-56755000	Weak transcription	NHDF-Ad	bronchial
36	chr4:56747800-56759600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:56747800-56759800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr4:56747800-56760000	Weak transcription	Fetal Brain Male	brain
39	chr4:56747800-56772800	Weak transcription	NHEK	skin
40	chr4:56748000-56751200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:56748000-56758600	Weak transcription	Fetal Brain Female	brain
42	chr4:56748000-56763400	Weak transcription	Brain Angular Gyrus	brain
43	chr4:56748000-56763800	Weak transcription	Esophagus	oesophagus
44	chr4:56748000-56770000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:56748000-56772000	Weak transcription	NHLF	lung
46	chr4:56748000-56773200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr4:56748200-56756000	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:56748200-56758800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:56748200-56759000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:56748200-56760000	Weak transcription	Spleen	Spleen

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