Variant report

Variant	rs4026508
Chromosome Location	chr1:197536424-197536425
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197536074..197537804-chr1:197566047..197569001,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10754228	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10801620	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10922231	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs10922236	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10922252	0.92[ASN][1000 genomes]
rs10922259	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10922260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10922266	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1135810	0.90[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs12042609	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs12066841	0.81[ASN][1000 genomes]
rs1337166	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1345529	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap]
rs1923759	0.85[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs1998711	0.97[ASN][1000 genomes]
rs2111930	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2111934	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4026513	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4026514	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.84[ASN][1000 genomes]
rs4147323	0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4274099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4282851	0.93[ASN][1000 genomes]
rs4418639	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs4604725	0.90[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs4611052	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6428416	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6667685	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688289	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6691216	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7516153	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516481	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs7523627	0.96[ASN][1000 genomes]
rs7533766	0.83[ASN][1000 genomes]
rs7534863	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7548454	0.93[ASN][1000 genomes]
rs927510	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs9633354	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9658810	0.80[EUR][1000 genomes]
rs9787082	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv548872	chr1:197529218-197644581	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4026508	LHX2	trans	parietal	SCAN
rs4026508	DENND1B	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197478000-197541200	Weak transcription	Aorta	Aorta
2	chr1:197480200-197541200	Weak transcription	Esophagus	oesophagus
3	chr1:197480200-197541200	Weak transcription	Fetal Thymus	thymus
4	chr1:197480400-197541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:197503200-197541200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:197505600-197541000	Weak transcription	Pancreas	Pancrea
7	chr1:197506600-197537600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:197506800-197564600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:197508400-197602400	Weak transcription	Left Ventricle	heart
10	chr1:197525400-197541200	Weak transcription	Ovary	ovary
11	chr1:197526800-197563000	Weak transcription	Osteobl	bone
12	chr1:197529600-197541400	Weak transcription	Colonic Mucosa	Colon
13	chr1:197529800-197548800	Weak transcription	Right Ventricle	heart
14	chr1:197530400-197536600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:197530800-197541200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:197533400-197540200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:197535600-197537400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
18	chr1:197535600-197537800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
19	chr1:197535600-197538400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:197535600-197538800	ZNF genes & repeats	Dnd41	blood
21	chr1:197535600-197542200	Weak transcription	Small Intestine	intestine
22	chr1:197535800-197536800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:197535800-197536800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr1:197535800-197537000	ZNF genes & repeats	Primary T cells from cord blood	blood
25	chr1:197535800-197537000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
26	chr1:197535800-197537800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:197535800-197538200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:197535800-197538600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:197535800-197539000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:197535800-197539000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
31	chr1:197536000-197536800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:197536000-197537400	ZNF genes & repeats	Fetal Lung	lung
33	chr1:197536000-197538400	ZNF genes & repeats	Liver	Liver
34	chr1:197536200-197536600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:197536200-197541000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:197536400-197537000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr1:197536400-197537200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood

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