Variant report

Variant	rs2724717
Chromosome Location	chr3:137812693-137812694
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	POU5F1	chr3:137812349-137812717	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
DZIP1L	TF binding region

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1107422	0.94[ASN][1000 genomes]
rs11719358	0.87[ASN][1000 genomes]
rs13100360	0.97[ASN][1000 genomes]
rs1351446	0.88[ASN][1000 genomes]
rs1444577	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1444578	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1545816	0.97[ASN][1000 genomes]
rs1564496	0.90[ASN][1000 genomes]
rs17838821	0.97[ASN][1000 genomes]
rs179282	0.87[ASN][1000 genomes]
rs2170309	0.90[ASN][1000 genomes]
rs2246945	0.90[ASN][1000 genomes]
rs2589259	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2589260	0.81[EUR][1000 genomes]
rs2622697	0.90[ASN][1000 genomes]
rs2622698	0.88[ASN][1000 genomes]
rs2622704	0.89[ASN][1000 genomes]
rs2622705	0.89[ASN][1000 genomes]
rs2622706	0.89[ASN][1000 genomes]
rs2622707	0.89[ASN][1000 genomes]
rs2622709	0.92[ASN][1000 genomes]
rs2622710	0.92[ASN][1000 genomes]
rs2622711	0.93[ASN][1000 genomes]
rs2622714	0.96[ASN][1000 genomes]
rs2622715	0.96[ASN][1000 genomes]
rs2622716	0.96[ASN][1000 genomes]
rs2622717	0.96[ASN][1000 genomes]
rs2622718	0.96[ASN][1000 genomes]
rs2622719	0.97[ASN][1000 genomes]
rs2622720	0.97[ASN][1000 genomes]
rs2622724	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2622725	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2622726	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2622727	0.97[ASN][1000 genomes]
rs2622728	0.97[ASN][1000 genomes]
rs2622729	0.97[ASN][1000 genomes]
rs2622730	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622745	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2622746	0.90[ASN][1000 genomes]
rs2724679	0.82[ASN][1000 genomes]
rs2724687	0.88[ASN][1000 genomes]
rs2724693	0.96[ASN][1000 genomes]
rs2724694	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2724695	0.89[ASN][1000 genomes]
rs2724697	0.92[ASN][1000 genomes]
rs2724698	0.89[ASN][1000 genomes]
rs2724699	0.89[ASN][1000 genomes]
rs2724700	0.89[ASN][1000 genomes]
rs2724701	0.89[ASN][1000 genomes]
rs2724702	0.89[ASN][1000 genomes]
rs2724703	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2724704	0.89[ASN][1000 genomes]
rs2724705	0.89[ASN][1000 genomes]
rs2724706	0.89[ASN][1000 genomes]
rs2724707	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2724708	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2724713	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2724716	0.97[ASN][1000 genomes]
rs2724720	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2724721	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2724722	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2724723	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2724729	0.90[ASN][1000 genomes]
rs28480035	0.93[ASN][1000 genomes]
rs329381	0.97[ASN][1000 genomes]
rs329382	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs329383	0.96[ASN][1000 genomes]
rs329384	0.97[ASN][1000 genomes]
rs329385	0.97[ASN][1000 genomes]
rs329388	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs329389	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329390	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329391	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs365504	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs367439	0.97[ASN][1000 genomes]
rs374045	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs382629	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs384828	0.92[ASN][1000 genomes]
rs389697	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs390729	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405265	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405517	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs405602	0.92[ASN][1000 genomes]
rs407009	0.89[ASN][1000 genomes]
rs419075	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs425938	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs436145	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs442800	0.89[ASN][1000 genomes]
rs445025	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs446644	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs452195	0.89[ASN][1000 genomes]
rs453023	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4678403	0.90[ASN][1000 genomes]
rs618553	0.92[ASN][1000 genomes]
rs6809258	0.93[ASN][1000 genomes]
rs7613955	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629243	0.97[ASN][1000 genomes]
rs7639197	0.96[ASN][1000 genomes]
rs899983	0.94[ASN][1000 genomes]
rs9812778	0.88[ASN][1000 genomes]
rs9814877	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9834462	0.90[ASN][1000 genomes]
rs9834670	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9842648	0.89[ASN][1000 genomes]
rs9842918	0.92[ASN][1000 genomes]
rs9857908	0.89[ASN][1000 genomes]
rs9860229	0.90[ASN][1000 genomes]
rs9860630	0.86[ASN][1000 genomes]
rs9874211	0.87[ASN][1000 genomes]
rs996432	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007857	chr3:137767454-137843106	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137780000-137813400	Weak transcription	HUVEC	blood vessel
2	chr3:137781000-137833200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:137783200-137821200	Weak transcription	Colonic Mucosa	Colon
4	chr3:137792000-137820600	Weak transcription	Esophagus	oesophagus
5	chr3:137792400-137818200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:137801600-137820600	Weak transcription	Spleen	Spleen
7	chr3:137801600-137833200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:137801800-137815200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:137802200-137818200	Weak transcription	Hela-S3	cervix
10	chr3:137802400-137813200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:137802400-137823200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr3:137802600-137822200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr3:137803200-137812800	Weak transcription	Fetal Brain Female	brain
14	chr3:137803200-137815600	Weak transcription	Brain Substantia Nigra	brain
15	chr3:137803200-137833200	Weak transcription	Placenta	Placenta
16	chr3:137803400-137820200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:137803400-137822400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:137803600-137816200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:137803800-137813000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:137803800-137813600	Weak transcription	Liver	Liver
21	chr3:137805200-137823400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:137805200-137823400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:137805600-137829800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:137805800-137813200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:137805800-137813200	Weak transcription	Aorta	Aorta
26	chr3:137805800-137816400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:137805800-137816400	Weak transcription	Gastric	stomach
28	chr3:137805800-137819000	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:137805800-137820600	Weak transcription	Fetal Intestine Small	intestine
30	chr3:137805800-137822000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:137806000-137813200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:137806000-137813400	Weak transcription	Fetal Intestine Large	intestine
33	chr3:137806800-137813000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:137806800-137813600	Weak transcription	Lung	lung
35	chr3:137807000-137821600	Weak transcription	Brain Anterior Caudate	brain
36	chr3:137807000-137822200	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:137807400-137813200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:137807400-137813400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:137807400-137820600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:137807400-137820600	Weak transcription	Right Ventricle	heart
41	chr3:137807600-137818600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:137807600-137822000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:137807800-137818800	Weak transcription	Pancreas	Pancrea
44	chr3:137807800-137819600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:137808000-137813000	Weak transcription	Ovary	ovary
46	chr3:137808000-137814000	Strong transcription	Adipose Nuclei	Adipose
47	chr3:137808000-137821200	Weak transcription	HSMMtube	muscle
48	chr3:137808800-137813000	Weak transcription	HMEC	breast
49	chr3:137808800-137819600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:137808800-137830800	Weak transcription	NHEK	skin

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