Variant report

Variant	rs12042609
Chromosome Location	chr1:197477448-197477449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197468068..197470896-chr1:197476662..197478717,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10494756	0.93[ASN][1000 genomes]
rs10801607	0.83[EUR][1000 genomes]
rs10801609	0.90[ASN][1000 genomes]
rs10922231	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs10922236	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10922244	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10922259	0.80[EUR][1000 genomes]
rs10922260	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1135810	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs12026564	0.87[ASN][1000 genomes]
rs1337166	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1345529	0.85[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs1923759	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs2111930	0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs2287537	0.95[ASN][1000 genomes]
rs4026508	0.81[EUR][1000 genomes]
rs4026513	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4026514	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs4147323	0.85[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs4274099	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs4418639	0.80[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs4604725	0.85[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap]
rs6667685	0.80[EUR][1000 genomes]
rs6691216	0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs7516153	0.80[EUR][1000 genomes]
rs7534863	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs927510	0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs9658810	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9787082	0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][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
rs12042609	DENND1B	cis	parietal	SCAN
rs12042609	LHX2	trans	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197467200-197499000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:197472200-197477800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:197473800-197479200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:197474000-197481600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:197475000-197484800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:197475200-197479000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:197475400-197478800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:197475800-197478200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:197476200-197479600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:197476400-197478000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:197476400-197478000	Weak transcription	Dnd41	blood
12	chr1:197476400-197478800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:197476600-197478200	Weak transcription	Primary B cells from cord blood	blood
14	chr1:197476600-197478200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:197476600-197478200	Weak transcription	Adipose Nuclei	Adipose
16	chr1:197476600-197478800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:197476600-197479600	Weak transcription	Ovary	ovary
18	chr1:197476800-197478400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:197476800-197478400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:197476800-197479200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:197476800-197479200	Weak transcription	Fetal Lung	lung
22	chr1:197476800-197479200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:197476800-197479600	Weak transcription	Primary T cells from cord blood	blood
24	chr1:197476800-197479600	Weak transcription	Esophagus	oesophagus
25	chr1:197476800-197479600	Weak transcription	Left Ventricle	heart
26	chr1:197476800-197479600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:197476800-197482600	Weak transcription	Hela-S3	cervix
28	chr1:197476800-197483400	Weak transcription	Small Intestine	intestine
29	chr1:197476800-197484600	Weak transcription	Fetal Intestine Large	intestine
30	chr1:197477000-197479000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:197477200-197478800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:197477200-197479200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:197477400-197479000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:197477400-197479600	Weak transcription	Primary B cells from peripheral blood	blood

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