Variant report

Variant	rs2724693
Chromosome Location	chr3:137807259-137807260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1107422	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719358	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13100360	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1351446	0.89[ASN][1000 genomes]
rs1444577	0.81[ASN][1000 genomes]
rs1444578	0.80[ASN][1000 genomes]
rs1545816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1564496	0.86[ASN][1000 genomes]
rs17838821	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs179282	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2170309	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2246945	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2589259	0.81[ASN][1000 genomes]
rs2622697	0.86[ASN][1000 genomes]
rs2622698	0.89[ASN][1000 genomes]
rs2622704	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622706	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622707	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622710	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622713	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2622714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622715	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622716	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622718	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622720	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622724	0.86[ASN][1000 genomes]
rs2622725	0.86[ASN][1000 genomes]
rs2622726	0.86[ASN][1000 genomes]
rs2622727	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622728	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622729	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622730	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2622745	0.80[ASN][1000 genomes]
rs2622746	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2724679	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2724687	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2724694	0.96[ASN][1000 genomes]
rs2724695	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2724697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2724698	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2724699	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2724700	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2724701	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2724702	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2724703	0.90[ASN][1000 genomes]
rs2724704	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2724705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2724706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2724707	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2724708	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2724713	0.86[ASN][1000 genomes]
rs2724716	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2724717	0.96[ASN][1000 genomes]
rs2724720	0.86[ASN][1000 genomes]
rs2724721	0.86[ASN][1000 genomes]
rs2724722	0.86[ASN][1000 genomes]
rs2724723	0.86[ASN][1000 genomes]
rs2724729	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28480035	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs329381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs329382	0.89[ASN][1000 genomes]
rs329383	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs329384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs329385	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs329388	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs329389	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs329390	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs329391	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs365504	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs367439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs374045	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs382629	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs384828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs389697	0.88[ASN][1000 genomes]
rs390729	0.96[ASN][1000 genomes]
rs405265	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs405517	0.86[ASN][1000 genomes]
rs405602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs407009	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs419075	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs425938	0.90[ASN][1000 genomes]
rs436145	0.86[ASN][1000 genomes]
rs442800	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs445025	0.90[ASN][1000 genomes]
rs446644	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs452195	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs453023	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4678403	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs618553	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6809258	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7613955	0.96[ASN][1000 genomes]
rs7629243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7639197	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899983	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9812778	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9814877	0.86[ASN][1000 genomes]
rs9834462	0.91[ASN][1000 genomes]
rs9834670	0.86[ASN][1000 genomes]
rs9842648	0.91[ASN][1000 genomes]
rs9842918	0.88[ASN][1000 genomes]
rs9857908	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs9860229	0.91[ASN][1000 genomes]
rs9860630	0.88[ASN][1000 genomes]
rs9874211	0.83[ASN][1000 genomes]
rs996432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2724693	CLDN18	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137780000-137813400	Weak transcription	HUVEC	blood vessel
2	chr3:137780600-137811600	Weak transcription	Psoas Muscle	Psoas
3	chr3:137781000-137833200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:137783200-137811600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:137783200-137821200	Weak transcription	Colonic Mucosa	Colon
6	chr3:137792000-137820600	Weak transcription	Esophagus	oesophagus
7	chr3:137792400-137818200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:137796200-137811400	Weak transcription	Fetal Brain Male	brain
9	chr3:137801600-137820600	Weak transcription	Spleen	Spleen
10	chr3:137801600-137833200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:137801800-137807800	Weak transcription	NHEK	skin
12	chr3:137801800-137812600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:137801800-137815200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:137802200-137818200	Weak transcription	Hela-S3	cervix
15	chr3:137802400-137813200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:137802400-137823200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:137802600-137808800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:137802600-137822200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr3:137803200-137812200	Weak transcription	Brain Angular Gyrus	brain
20	chr3:137803200-137812800	Weak transcription	Fetal Brain Female	brain
21	chr3:137803200-137815600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:137803200-137833200	Weak transcription	Placenta	Placenta
23	chr3:137803400-137812600	Weak transcription	Brain Germinal Matrix	brain
24	chr3:137803400-137820200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:137803400-137822400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:137803600-137816200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:137803800-137813000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:137803800-137813600	Weak transcription	Liver	Liver
29	chr3:137805000-137808000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:137805200-137807400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:137805200-137807400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:137805200-137807400	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:137805200-137807400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:137805200-137807400	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:137805200-137807400	Strong transcription	Right Ventricle	heart
36	chr3:137805200-137807400	Strong transcription	NH-A	brain
37	chr3:137805200-137807600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:137805200-137807600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:137805200-137807600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:137805200-137807600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:137805200-137807600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:137805200-137807600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:137805200-137807600	Strong transcription	Left Ventricle	heart
44	chr3:137805200-137807600	Strong transcription	NHDF-Ad	bronchial
45	chr3:137805200-137807600	Strong transcription	NHLF	lung
46	chr3:137805200-137807600	Strong transcription	Osteobl	bone
47	chr3:137805200-137807800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:137805200-137807800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:137805200-137807800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:137805200-137807800	Strong transcription	Fetal Muscle Trunk	muscle

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