Variant report

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:86901718-86902107	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86898686..86902993-chr1:86903541..86907633,5	K562	blood:

Variant related genes	Relation type
CLCA2	TF binding region
ENSG00000137975	Chromatin interaction

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

rs_ID	r²[population]
rs10493790	0.91[CEU][hapmap]
rs10873785	0.88[ASN][1000 genomes]
rs11161812	0.86[CEU][hapmap]
rs11161816	0.91[CEU][hapmap]
rs11161831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158833	0.91[CEU][hapmap]
rs1182098	0.81[CEU][hapmap]
rs1182099	0.81[CEU][hapmap]
rs12145243	0.91[CEU][hapmap]
rs12403033	0.85[CEU][hapmap]
rs12406320	0.84[CEU][hapmap]
rs1413431	0.91[CEU][hapmap]
rs17409304	0.91[CEU][hapmap]
rs17449526	0.91[CEU][hapmap]
rs1814203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272493	0.80[CEU][hapmap]
rs272497	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs272500	0.81[CEU][hapmap]
rs272514	0.81[CEU][hapmap]
rs3737673	0.91[CEU][hapmap]
rs3765983	0.94[CEU][hapmap]
rs3820039	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs421105	0.81[CEU][hapmap]
rs5026277	0.85[CEU][hapmap]
rs57160573	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72720116	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72720130	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518184	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12146009	CLCA2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86890600-86903000	Weak transcription	Esophagus	oesophagus
2	chr1:86896600-86902600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:86896600-86914400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:86897200-86922600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:86897200-86922800	Strong transcription	HMEC	breast
6	chr1:86897400-86906200	Strong transcription	NHEK	skin
7	chr1:86897400-86916000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:86900200-86902000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:86900200-86902200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:86900800-86902400	Weak transcription	Gastric	stomach
11	chr1:86901200-86902000	Enhancers	Fetal Lung	lung
12	chr1:86901400-86902400	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr1:86901600-86902000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:86901800-86902000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr1:86901800-86902200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:86901800-86902200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:86901800-86902200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:86901800-86902400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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