Variant report

Variant	rs10873682
Chromosome Location	chr1:85497812-85497813
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	chr1:85154869..85157586-chr1:85496519..85498325,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117155	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10782534	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs10782536	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10873669	0.86[EUR][1000 genomes]
rs10873670	0.86[EUR][1000 genomes]
rs10873672	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes]
rs10873676	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10873677	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10873678	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10873679	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10873683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161495	0.86[EUR][1000 genomes]
rs11161496	0.85[EUR][1000 genomes]
rs11161497	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11161498	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11161499	0.86[EUR][1000 genomes]
rs11161501	0.81[EUR][1000 genomes]
rs11161502	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11161503	0.82[EUR][1000 genomes]
rs11161504	0.82[EUR][1000 genomes]
rs11161505	0.82[EUR][1000 genomes]
rs11161513	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161514	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161525	0.80[CHB][hapmap]
rs11161526	0.81[CHB][hapmap]
rs11485283	0.85[EUR][1000 genomes]
rs11485284	0.86[EUR][1000 genomes]
rs11799517	0.82[EUR][1000 genomes]
rs11804248	0.82[EUR][1000 genomes]
rs12022421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12030990	0.81[CHB][hapmap]
rs12062414	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12063120	0.81[CHB][hapmap]
rs12091131	0.86[EUR][1000 genomes]
rs12130357	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12138711	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12730688	0.86[EUR][1000 genomes]
rs1439130	0.84[EUR][1000 genomes]
rs1837328	0.82[EUR][1000 genomes]
rs2389792	0.82[EUR][1000 genomes]
rs2389793	0.82[EUR][1000 genomes]
rs2486755	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs3850430	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3861690	0.82[EUR][1000 genomes]
rs3895846	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs486751	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs488710	0.86[EUR][1000 genomes]
rs4907017	0.86[EUR][1000 genomes]
rs4907018	0.86[EUR][1000 genomes]
rs4907118	0.86[EUR][1000 genomes]
rs4907123	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4907125	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs495786	0.85[EUR][1000 genomes]
rs499539	0.86[EUR][1000 genomes]
rs513430	0.86[EUR][1000 genomes]
rs515303	0.85[EUR][1000 genomes]
rs530486	0.86[EUR][1000 genomes]
rs531423	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs589653	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes]
rs600536	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes]
rs603746	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs625045	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs631267	0.86[EUR][1000 genomes]
rs632545	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs648660	0.86[EUR][1000 genomes]
rs650529	0.82[EUR][1000 genomes]
rs651916	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes]
rs6576736	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs662948	0.86[EUR][1000 genomes]
rs6677091	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6685363	0.86[EUR][1000 genomes]
rs668860	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes]
rs6690464	0.82[YRI][hapmap]
rs6690583	0.82[YRI][hapmap]
rs6691674	0.86[EUR][1000 genomes]
rs6691970	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6700622	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6701779	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs677476	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs679167	0.86[EUR][1000 genomes]
rs726708	0.82[EUR][1000 genomes]
rs7516329	0.82[EUR][1000 genomes]
rs7516610	0.82[EUR][1000 genomes]
rs7516625	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7519134	0.81[EUR][1000 genomes]
rs7522851	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs7534574	0.81[CHB][hapmap]
rs7541684	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7549346	0.86[EUR][1000 genomes]
rs7552445	0.81[EUR][1000 genomes]
rs7553886	0.82[EUR][1000 genomes]

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	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10873682	MCOLN2	cis	parietal	SCAN
rs10873682	MCOLN2	cis	multi-tissue	Pritchard
rs10873682	MCOLN2	cis	Artery Tibial	GTEx
rs10873682	MCOLN2	cis	lymphoblastoid	seeQTL
rs10873682	MCOLN2	cis	Adipose Subcutaneous	GTEx
rs10873682	LMO4	cis	cerebellum	SCAN
rs10873682	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL
rs10873682	MCOLN2	cis	Thyroid	GTEx
rs10873682	MCOLN3	cis	Thyroid	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85485400-85513000	Weak transcription	Pancreas	Pancrea
2	chr1:85485800-85505200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:85486000-85513000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:85486400-85499200	Weak transcription	NHDF-Ad	bronchial
5	chr1:85486400-85500400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:85489000-85500000	Weak transcription	Adipose Nuclei	Adipose
7	chr1:85493000-85498200	Strong transcription	Fetal Intestine Large	intestine
8	chr1:85493000-85501000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:85493600-85498800	Weak transcription	GM12878-XiMat	blood
10	chr1:85494000-85498000	Weak transcription	Osteobl	bone
11	chr1:85495000-85512800	Weak transcription	HMEC	breast
12	chr1:85496000-85499000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:85496000-85500000	Weak transcription	Right Atrium	heart
14	chr1:85496400-85498800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:85496800-85512400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:85497000-85501800	Weak transcription	Fetal Intestine Small	intestine

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