Variant report

Variant	rs17013759
Chromosome Location	chr4:129752379-129752380
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	REST	chr4:129752239-129753520	H1-neurons	neurons:	n/a	n/a
2	FOXA1	chr4:129752247-129752911	HepG2	liver:	n/a	n/a
3	RELA	chr4:129751938-129754356	GM18951	blood:	n/a	n/a
4	RUNX3	chr4:129751833-129752478	GM12878	blood:	n/a	n/a
5	BHLHE40	chr4:129752130-129752573	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:129751812-129753954	GM12891	blood:	n/a	n/a
7	REST	chr4:129752349-129753483	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr4:129751847-129752654	H1-hESC	embryonic stem cell:	n/a	n/a
9	EBF1	chr4:129751978-129752703	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:129751584-129753214	H1-hESC	embryonic stem cell:	n/a	n/a
11	WRNIP1	chr4:129752049-129752627	GM12878	blood:	n/a	n/a
12	RELA	chr4:129751922-129753648	GM19099	blood:	n/a	n/a
13	FOXA1	chr4:129752366-129752924	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129731357..129734214-chr4:129752200..129753715,2	K562	blood:

Variant related genes	Relation type
JADE1	TF binding region
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs17013725	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013730	1.00[EUR][1000 genomes]
rs17013733	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013765	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013766	1.00[EUR][1000 genomes]
rs17013775	1.00[EUR][1000 genomes]
rs17013777	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013779	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013786	1.00[EUR][1000 genomes]
rs17013787	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013789	1.00[EUR][1000 genomes]
rs17013807	1.00[EUR][1000 genomes]
rs17013811	1.00[EUR][1000 genomes]
rs17013813	1.00[EUR][1000 genomes]
rs17013815	1.00[EUR][1000 genomes]
rs17013817	1.00[EUR][1000 genomes]
rs17013825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013827	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013835	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013841	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013844	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013852	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013854	1.00[EUR][1000 genomes]
rs17013857	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013862	1.00[EUR][1000 genomes]
rs17013866	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013872	1.00[EUR][1000 genomes]
rs17013873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013877	1.00[EUR][1000 genomes]
rs17013882	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013895	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013898	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013903	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17303098	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2004378	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28635430	1.00[EUR][1000 genomes]
rs57153966	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57547066	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58296567	1.00[EUR][1000 genomes]
rs58580868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58593491	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58728331	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58755790	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58922070	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58981205	1.00[EUR][1000 genomes]
rs59682469	1.00[EUR][1000 genomes]
rs60787284	1.00[EUR][1000 genomes]
rs61306978	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61620977	1.00[EUR][1000 genomes]
rs61696721	1.00[EUR][1000 genomes]
rs6813405	1.00[EUR][1000 genomes]
rs6827804	1.00[EUR][1000 genomes]
rs6848234	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6850940	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6855813	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73846991	1.00[EUR][1000 genomes]
rs73850004	1.00[EUR][1000 genomes]
rs7682356	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 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	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
2	chr4:129746600-129752800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:129746600-129761800	Strong transcription	Dnd41	blood
4	chr4:129746800-129757000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:129746800-129770200	Weak transcription	HMEC	breast
6	chr4:129747000-129766600	Weak transcription	NHEK	skin
7	chr4:129747400-129752400	Weak transcription	HSMMtube	muscle
8	chr4:129747400-129754200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr4:129747400-129756600	Weak transcription	Esophagus	oesophagus
10	chr4:129747400-129761600	Weak transcription	Placenta	Placenta
11	chr4:129748000-129761600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:129749000-129754200	Genic enhancers	H1 Cell Line	embryonic stem cell
13	chr4:129749600-129752400	Enhancers	H9 Cell Line	embryonic stem cell
14	chr4:129749600-129752400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:129750000-129753200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:129751000-129752400	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr4:129751400-129752600	Enhancers	Primary T cells fromperipheralblood	blood
18	chr4:129751400-129752600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:129751400-129752800	Enhancers	Lung	lung
20	chr4:129751400-129753400	Enhancers	Psoas Muscle	Psoas
21	chr4:129751400-129753600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
22	chr4:129751600-129752400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:129751600-129752400	Enhancers	Brain Anterior Caudate	brain
24	chr4:129751600-129752400	Enhancers	HepG2	liver
25	chr4:129751600-129752600	Flanking Active TSS	GM12878-XiMat	blood
26	chr4:129751600-129752800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr4:129751600-129753000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:129751600-129753000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:129751600-129753000	Enhancers	Primary B cells from peripheral blood	blood
30	chr4:129751600-129753000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr4:129751600-129753000	Genic enhancers	Thymus	Thymus
32	chr4:129751600-129753200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:129751600-129753200	Enhancers	Adipose Nuclei	Adipose
34	chr4:129751600-129753200	Enhancers	Gastric	stomach
35	chr4:129751600-129753200	Enhancers	Left Ventricle	heart
36	chr4:129751600-129753200	Enhancers	Ovary	ovary
37	chr4:129751600-129753200	Genic enhancers	K562	blood
38	chr4:129751600-129753400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr4:129751600-129753400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr4:129751600-129753400	Enhancers	Right Ventricle	heart
41	chr4:129751600-129753400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr4:129751600-129753600	Enhancers	Stomach Mucosa	stomach
43	chr4:129751600-129753800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:129751600-129754000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:129751600-129754200	Enhancers	Small Intestine	intestine
46	chr4:129751600-129754800	Enhancers	Pancreas	Pancrea
47	chr4:129751600-129757200	Genic enhancers	Fetal Intestine Small	intestine
48	chr4:129751800-129752400	Genic enhancers	Primary T cells from cord blood	blood
49	chr4:129751800-129752600	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr4:129751800-129752600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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