Variant report

Variant	rs2287537
Chromosome Location	chr1:197482265-197482266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197481645..197483938-chr1:197564288..197566094,2	K562	blood:
2	chr1:197466870..197468517-chr1:197480625..197483174,2	K562	blood:
3	chr1:197473765..197476231-chr1:197480275..197482874,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10494756	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10801607	0.83[ASN][1000 genomes]
rs10801609	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10922231	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs10922236	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10922244	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10922252	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10922260	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1135810	0.89[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[ASN][1000 genomes]
rs12026564	0.82[ASN][1000 genomes]
rs12042609	0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.95[ASN][1000 genomes]
rs1337166	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1345529	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs1923759	0.85[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs1998711	0.82[EUR][1000 genomes]
rs2111930	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs4026513	0.86[ASN][1000 genomes]
rs4026514	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4147323	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs4274099	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4418639	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs4604725	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6691216	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs7523627	0.82[EUR][1000 genomes]
rs7534863	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs927510	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs9658810	0.91[ASN][1000 genomes]
rs9787082	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]

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	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521647	chr1:197464448-197529218	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv4010	chr1:197471463-197511397	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2287537	LHX2	trans	parietal	SCAN
rs2287537	DENND1B	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197467200-197499000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:197475000-197484800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:197476800-197482600	Weak transcription	Hela-S3	cervix
4	chr1:197476800-197483400	Weak transcription	Small Intestine	intestine
5	chr1:197476800-197484600	Weak transcription	Fetal Intestine Large	intestine
6	chr1:197478000-197483800	Weak transcription	Right Ventricle	heart
7	chr1:197478000-197541200	Weak transcription	Aorta	Aorta
8	chr1:197478200-197482600	Weak transcription	Lung	lung
9	chr1:197478600-197491200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:197480000-197482400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:197480000-197484600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:197480000-197489600	Weak transcription	Psoas Muscle	Psoas
13	chr1:197480000-197489800	Weak transcription	Brain Anterior Caudate	brain
14	chr1:197480000-197491000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:197480000-197535800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:197480200-197485400	Weak transcription	Thymus	Thymus
17	chr1:197480200-197485600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:197480200-197489200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:197480200-197541200	Weak transcription	Esophagus	oesophagus
20	chr1:197480200-197541200	Weak transcription	Fetal Thymus	thymus
21	chr1:197480400-197482600	Weak transcription	K562	blood
22	chr1:197480400-197482800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:197480400-197484000	Weak transcription	Fetal Lung	lung
24	chr1:197480400-197485800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:197480400-197487200	Weak transcription	Ovary	ovary
26	chr1:197480400-197541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:197480600-197486800	Weak transcription	Fetal Brain Male	brain
28	chr1:197481000-197507000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:197481200-197482800	Weak transcription	NHDF-Ad	bronchial
30	chr1:197481200-197483800	Weak transcription	Liver	Liver
31	chr1:197481200-197484600	Weak transcription	Fetal Heart	heart
32	chr1:197481200-197484800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:197481200-197485800	Weak transcription	Primary B cells from cord blood	blood
34	chr1:197481200-197491200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:197481200-197503400	Weak transcription	Primary T cells from cord blood	blood
36	chr1:197481200-197504200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:197481200-197507200	Weak transcription	Dnd41	blood
38	chr1:197481200-197508000	Weak transcription	Left Ventricle	heart
39	chr1:197481200-197513400	Weak transcription	Adipose Nuclei	Adipose
40	chr1:197481400-197483600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr1:197481400-197487800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:197481400-197503600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:197481400-197529600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:197481800-197482600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:197481800-197483600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:197482000-197483600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr1:197482000-197484200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr1:197482000-197508000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:197482000-197508000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr1:197482200-197483600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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