Variant report

Variant	rs2389969
Chromosome Location	chr1:86069153-86069154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:86045233..86051336-chr1:86057804..86069814,19	K562	blood:
2	chr1:86044046..86050058-chr1:86065602..86074449,16	MCF-7	breast:
3	chr1:86067788..86069598-chr1:86069646..86072509,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142871	Chromatin interaction
ENSG00000272691	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10873708	0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10873710	0.85[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11578464	0.85[ASW][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12120700	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4370804	0.92[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4949896	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4949911	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4949912	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4949914	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4949915	0.82[YRI][hapmap]
rs721471	0.83[MKK][hapmap]
rs9658595	0.94[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2389969	CLCA2	cis	cerebellum	SCAN
rs2389969	LPHN2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86048800-86081200	Weak transcription	Gastric	stomach
2	chr1:86053800-86071400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:86063000-86069400	Weak transcription	Fetal Lung	lung
4	chr1:86064000-86072600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:86065000-86071600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:86065200-86071400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:86065200-86072000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:86066600-86077000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:86068000-86074600	Enhancers	Fetal Intestine Small	intestine
10	chr1:86068200-86070600	Enhancers	Fetal Stomach	stomach
11	chr1:86068400-86072000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:86068400-86072400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:86068400-86074800	Enhancers	Fetal Intestine Large	intestine
14	chr1:86068600-86070400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:86068800-86070000	Enhancers	HepG2	liver
16	chr1:86068800-86071400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:86068800-86071400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:86068800-86071400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:86068800-86072000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:86068800-86072200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:86069000-86070000	Enhancers	Stomach Smooth Muscle	stomach
22	chr1:86069000-86071800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:86069000-86072000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:86069000-86072600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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