Variant report

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10157996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10752948	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10911706	0.92[EUR][1000 genomes]
rs10911707	0.87[CHD][hapmap]
rs10911711	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2207517	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2207518	0.90[EUR][1000 genomes]
rs2207519	0.90[EUR][1000 genomes]
rs2295212	0.92[EUR][1000 genomes]
rs4651253	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6424975	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs6659669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6665186	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs6679327	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6682074	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6689206	0.91[EUR][1000 genomes]
rs7519628	0.82[ASN][1000 genomes]
rs7548599	0.89[EUR][1000 genomes]
rs9988622	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	esv2756872	chr1:185293197-185345771	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2758981	chr1:185293197-185345771	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6424976	LHX4	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185308800-185317600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:185310800-185318600	Enhancers	HepG2	liver
3	chr1:185313200-185317400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:185313800-185327800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:185314200-185318600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:185315200-185317400	Enhancers	Primary T cells from cord blood	blood
7	chr1:185315600-185318400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:185315600-185318400	Weak transcription	Stomach Mucosa	stomach
9	chr1:185315600-185319600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:185316400-185318000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:185316600-185317600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:185317200-185317400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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