Variant report

Variant	rs17013744
Chromosome Location	chr4:129750460-129750461
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	POLR2A	chr4:129750081-129750544	H1-hESC	embryonic stem cell:	n/a	n/a
2	STAT1	chr4:129750273-129750473	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:129750035-129750463	A549	lung:	n/a	n/a
4	POLR2A	chr4:129747776-129750545	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
JADE1	TF binding region

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

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

rs_ID	r²[population]
rs17013725	0.90[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013730	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013733	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013736	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013759	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013765	1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013766	1.00[EUR][1000 genomes]
rs17013775	1.00[EUR][1000 genomes]
rs17013777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013779	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013786	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013787	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013789	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013807	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013811	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013813	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013815	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013817	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013827	1.00[ASW][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013835	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013841	1.00[ASW][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013847	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013848	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013849	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013852	1.00[ASW][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013854	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013857	1.00[ASW][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013862	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013866	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013872	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013873	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013877	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013882	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013894	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013895	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013899	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013903	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17303098	1.00[ASW][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2004378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28635430	1.00[EUR][1000 genomes]
rs57153966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57547066	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58296567	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58580868	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58593491	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58728331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58755790	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58922070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58981205	1.00[EUR][1000 genomes]
rs59682469	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60787284	1.00[EUR][1000 genomes]
rs61306978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61620977	1.00[EUR][1000 genomes]
rs61696721	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6813405	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6827804	0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6848234	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6850940	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6855813	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];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[YRI][hapmap];1.00[AFR][1000 genomes];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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129734400-129751600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
3	chr4:129735400-129752200	Weak transcription	Fetal Brain Female	brain
4	chr4:129741800-129752000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:129744800-129751600	Weak transcription	HUVEC	blood vessel
6	chr4:129745000-129751200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr4:129746400-129751200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
8	chr4:129746600-129750600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
9	chr4:129746600-129751800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:129746600-129752000	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr4:129746600-129752800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:129746600-129761800	Strong transcription	Dnd41	blood
13	chr4:129746800-129751800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:129746800-129757000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:129746800-129770200	Weak transcription	HMEC	breast
16	chr4:129747000-129751600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:129747000-129752000	Weak transcription	Fetal Brain Male	brain
18	chr4:129747000-129752200	Weak transcription	Hela-S3	cervix
19	chr4:129747000-129766600	Weak transcription	NHEK	skin
20	chr4:129747200-129751800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:129747200-129751800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:129747200-129752000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:129747400-129751600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:129747400-129751600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:129747400-129751600	Weak transcription	Stomach Mucosa	stomach
26	chr4:129747400-129751600	Weak transcription	Thymus	Thymus
27	chr4:129747400-129751800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr4:129747400-129751800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:129747400-129752000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr4:129747400-129752000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:129747400-129752000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:129747400-129752000	Weak transcription	NH-A	brain
33	chr4:129747400-129752200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:129747400-129752200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:129747400-129752400	Weak transcription	HSMMtube	muscle
36	chr4:129747400-129754200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr4:129747400-129756600	Weak transcription	Esophagus	oesophagus
38	chr4:129747400-129761600	Weak transcription	Placenta	Placenta
39	chr4:129747600-129751600	Weak transcription	Brain Anterior Caudate	brain
40	chr4:129747600-129751600	Weak transcription	Gastric	stomach
41	chr4:129747600-129751800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr4:129747600-129751800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:129747600-129752000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr4:129747600-129752000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr4:129748000-129750600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:129748000-129751200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr4:129748000-129761600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr4:129748200-129751600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr4:129748200-129751800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:129748200-129752000	Weak transcription	Brain Angular Gyrus	brain

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