Variant report

Variant	rs2724729
Chromosome Location	chr3:137832043-137832044
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1107422	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11719358	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13100360	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1351446	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1545816	0.86[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1564496	0.95[ASN][1000 genomes]
rs17838821	0.80[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs179282	0.87[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2170309	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2246945	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2622697	0.95[ASN][1000 genomes]
rs2622698	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2622704	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2622705	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2622706	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2622707	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2622709	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622710	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622711	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2622713	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2622714	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2622715	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2622716	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2622717	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2622718	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2622719	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622720	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622727	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622728	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622729	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622730	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2622745	0.88[ASN][1000 genomes]
rs2622746	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724679	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2724687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2724693	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]
rs2724694	0.87[ASN][1000 genomes]
rs2724695	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2724697	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2724698	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724699	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724700	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724701	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724702	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724703	0.82[ASN][1000 genomes]
rs2724704	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724705	0.86[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724706	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724707	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2724708	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2724716	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2724717	0.90[ASN][1000 genomes]
rs28480035	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329381	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs329382	0.85[ASN][1000 genomes]
rs329383	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs329384	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs329385	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs329388	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs329389	0.87[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs329390	0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs329391	0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs365504	0.80[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs367439	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs374045	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs382629	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs384828	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs390729	0.90[ASN][1000 genomes]
rs405265	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs405602	0.86[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs407009	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs419075	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs425938	0.82[ASN][1000 genomes]
rs442800	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs445025	0.82[ASN][1000 genomes]
rs446644	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs452195	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs453023	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4678403	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs618553	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6809258	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7613955	0.90[ASN][1000 genomes]
rs7629243	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7639197	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs899983	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9812778	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9834462	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9842648	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9842918	0.96[ASN][1000 genomes]
rs9857908	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];0.99[ASN][1000 genomes]
rs9860229	1.00[ASN][1000 genomes]
rs9860630	0.96[ASN][1000 genomes]
rs9874211	0.91[ASN][1000 genomes]
rs996432	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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
rs2724729	CLDN18	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137781000-137833200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:137801600-137833200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:137803200-137833200	Weak transcription	Placenta	Placenta
4	chr3:137811800-137833400	Weak transcription	Fetal Brain Male	brain
5	chr3:137812600-137833200	Weak transcription	Brain Angular Gyrus	brain
6	chr3:137813800-137833000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:137814000-137832200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:137814000-137833000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:137814000-137833600	Weak transcription	Liver	Liver
10	chr3:137814200-137832400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:137814200-137833200	Weak transcription	HUVEC	blood vessel
12	chr3:137816800-137833000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:137819400-137832200	Weak transcription	Stomach Mucosa	stomach
14	chr3:137820000-137832200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:137821000-137833200	Weak transcription	Fetal Intestine Small	intestine
16	chr3:137821600-137833000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:137822200-137832400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:137822400-137833200	Weak transcription	Brain Anterior Caudate	brain
19	chr3:137822600-137832400	Weak transcription	Esophagus	oesophagus
20	chr3:137822600-137833000	Weak transcription	HSMMtube	muscle
21	chr3:137822600-137833200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:137822800-137832200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:137822800-137832200	Weak transcription	Colonic Mucosa	Colon
24	chr3:137822800-137833000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:137822800-137833200	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:137822800-137833200	Weak transcription	Fetal Brain Female	brain
27	chr3:137823000-137832200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:137823000-137832200	Weak transcription	Aorta	Aorta
29	chr3:137823000-137832200	Weak transcription	Ovary	ovary
30	chr3:137823000-137832200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:137823000-137832400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:137823000-137833200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:137823000-137833200	Weak transcription	Lung	lung
34	chr3:137823000-137833400	Weak transcription	Gastric	stomach
35	chr3:137823200-137832400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:137823200-137832400	Weak transcription	Fetal Lung	lung
37	chr3:137823200-137833200	Weak transcription	Pancreas	Pancrea
38	chr3:137823200-137833200	Weak transcription	Spleen	Spleen
39	chr3:137823400-137832200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:137823600-137832200	Weak transcription	Left Ventricle	heart
41	chr3:137823600-137833200	Weak transcription	Right Ventricle	heart
42	chr3:137827800-137832400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:137830400-137832200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:137830400-137833000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:137830400-137833000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:137830800-137832200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:137830800-137832400	Weak transcription	Fetal Stomach	stomach
48	chr3:137831200-137832200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:137831200-137832200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:137831200-137832200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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