Variant report

Variant	rs441539
Chromosome Location	chr6:15764638-15764639
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	chr6:15763498..15765929-chr6:15906777..15908450,2	MCF-7	breast:
2	chr6:15759762..15765920-chr6:16126887..16131377,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000007944	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11751763	0.85[EUR][1000 genomes]
rs11753586	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs11759386	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13199464	0.89[CEU][hapmap]
rs16876927	0.96[ASN][1000 genomes]
rs16876933	0.96[ASN][1000 genomes]
rs16876977	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs1887604	0.85[CHB][hapmap];0.97[ASN][1000 genomes]
rs1927573	0.96[ASN][1000 genomes]
rs1927574	0.96[ASN][1000 genomes]
rs1927578	0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs2181435	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs220888	0.89[CHB][hapmap]
rs34030405	0.85[EUR][1000 genomes]
rs34080473	0.86[EUR][1000 genomes]
rs34669273	0.85[EUR][1000 genomes]
rs35110594	0.85[EUR][1000 genomes]
rs35835933	0.85[EUR][1000 genomes]
rs372993	0.87[JPT][hapmap]
rs374876	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs387754	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs388044	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs389429	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs399391	0.89[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs399732	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs400543	0.89[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs401126	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs407288	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs421665	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs421918	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs443804	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs56135160	0.87[EUR][1000 genomes]
rs563398	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs6459413	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs6933904	0.89[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs7738190	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs7739825	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7760793	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs9349987	0.94[ASN][1000 genomes]
rs9358068	0.97[ASN][1000 genomes]
rs9367881	0.96[ASN][1000 genomes]
rs9370827	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs9370828	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs9383075	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9383076	0.88[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9383077	0.98[ASN][1000 genomes]
rs9383078	0.89[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs9383079	0.89[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs9396602	0.99[ASN][1000 genomes]
rs9396604	0.89[CHB][hapmap];0.88[JPT][hapmap]

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	nsv428136	chr6:15595640-15781241	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2762581	chr6:15763793-15774802	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs441539	MGRN1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15759200-15770000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:15762200-15782000	Weak transcription	Pancreas	Pancrea
3	chr6:15763200-15766000	Enhancers	Fetal Intestine Large	intestine
4	chr6:15763400-15765200	Enhancers	Liver	Liver
5	chr6:15763400-15765600	Enhancers	Fetal Intestine Small	intestine
6	chr6:15763600-15764800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:15763600-15764800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:15763600-15764800	Enhancers	Adipose Nuclei	Adipose
9	chr6:15763600-15764800	Enhancers	Fetal Kidney	kidney
10	chr6:15763600-15765000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:15763600-15765000	Enhancers	Duodenum Mucosa	Duodenum
12	chr6:15763600-15765000	Enhancers	Fetal Lung	lung
13	chr6:15763600-15765600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr6:15763800-15764800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:15763800-15764800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:15763800-15764800	Enhancers	Fetal Heart	heart
17	chr6:15763800-15764800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr6:15763800-15765000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:15764200-15764800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:15764200-15765000	Enhancers	Gastric	stomach
21	chr6:15764400-15765000	Enhancers	Rectal Smooth Muscle	rectum
22	chr6:15764400-15768800	Weak transcription	K562	blood
23	chr6:15764600-15765000	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr6:15764600-15766200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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