Variant report

Variant	rs6853342
Chromosome Location	chr4:152487829-152487830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10857261	0.86[EUR][1000 genomes]
rs11099813	0.83[EUR][1000 genomes]
rs11099818	0.89[EUR][1000 genomes]
rs11723643	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11726171	0.83[EUR][1000 genomes]
rs11726222	0.89[EUR][1000 genomes]
rs11726545	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729514	0.89[EUR][1000 genomes]
rs11729871	0.81[EUR][1000 genomes]
rs11730733	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11734176	0.83[EUR][1000 genomes]
rs11735143	0.89[EUR][1000 genomes]
rs11736261	0.83[EUR][1000 genomes]
rs11736961	0.89[EUR][1000 genomes]
rs11934818	0.89[EUR][1000 genomes]
rs11947720	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12054502	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12498556	0.89[EUR][1000 genomes]
rs12498878	0.89[EUR][1000 genomes]
rs12502212	0.89[EUR][1000 genomes]
rs12504273	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508678	0.89[EUR][1000 genomes]
rs12511280	0.83[EUR][1000 genomes]
rs1366908	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1372979	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1443085	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17027716	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17275584	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17275605	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17275612	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1992517	0.89[EUR][1000 genomes]
rs28447105	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28463438	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28498882	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28672085	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28715753	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3172567	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35588363	0.81[EUR][1000 genomes]
rs36083376	0.89[EUR][1000 genomes]
rs3811748	0.83[EUR][1000 genomes]
rs3811749	0.83[EUR][1000 genomes]
rs3934474	0.89[EUR][1000 genomes]
rs4371601	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4622982	0.87[EUR][1000 genomes]
rs56092201	0.89[EUR][1000 genomes]
rs56763519	0.86[EUR][1000 genomes]
rs57272881	0.89[EUR][1000 genomes]
rs57348790	0.82[EUR][1000 genomes]
rs57556564	0.83[EUR][1000 genomes]
rs58443173	0.83[EUR][1000 genomes]
rs58863309	0.83[EUR][1000 genomes]
rs58961701	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59731141	0.89[EUR][1000 genomes]
rs59744221	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59777523	0.83[EUR][1000 genomes]
rs59811197	0.87[EUR][1000 genomes]
rs59984665	0.89[EUR][1000 genomes]
rs60055392	0.83[EUR][1000 genomes]
rs60077220	0.89[EUR][1000 genomes]
rs60122169	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60169090	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60707008	0.89[EUR][1000 genomes]
rs61294884	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61302767	0.89[EUR][1000 genomes]
rs61630225	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535802	0.89[EUR][1000 genomes]
rs6535805	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6813289	0.83[EUR][1000 genomes]
rs6826318	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6832899	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6835310	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838608	0.87[EUR][1000 genomes]
rs6839738	0.83[EUR][1000 genomes]
rs6844169	0.89[EUR][1000 genomes]
rs6845067	0.89[EUR][1000 genomes]
rs6846013	0.89[EUR][1000 genomes]
rs6846759	0.81[EUR][1000 genomes]
rs6851305	0.83[EUR][1000 genomes]
rs6856392	0.87[EUR][1000 genomes]
rs6858573	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73861275	0.83[EUR][1000 genomes]
rs73861826	0.86[EUR][1000 genomes]
rs73861827	0.86[EUR][1000 genomes]
rs73862055	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73862076	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73862080	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73862085	0.80[EUR][1000 genomes]
rs73864013	0.86[EUR][1000 genomes]
rs7653926	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655466	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662214	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7662713	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664074	0.89[EUR][1000 genomes]
rs7671456	0.83[EUR][1000 genomes]
rs7675933	0.83[EUR][1000 genomes]
rs7677528	0.89[EUR][1000 genomes]
rs7684972	0.83[EUR][1000 genomes]
rs7690773	0.83[EUR][1000 genomes]
rs7699787	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9683881	0.83[EUR][1000 genomes]
rs9917912	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1025192	chr4:152202627-152498890	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537307	chr4:152202627-152498890	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv881342	chr4:152363772-152560449	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv830114	chr4:152401288-152548606	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6853342	PET112L	cis	brain	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152476600-152494800	Weak transcription	HMEC	breast
2	chr4:152476600-152526600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:152477600-152494400	Weak transcription	NHEK	skin
4	chr4:152484400-152488800	Enhancers	Fetal Intestine Large	intestine
5	chr4:152484800-152490800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:152484800-152518600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:152485200-152496400	Weak transcription	Colonic Mucosa	Colon
8	chr4:152485600-152509600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:152485800-152489200	Weak transcription	Psoas Muscle	Psoas
10	chr4:152485800-152490200	Weak transcription	Pancreas	Pancrea
11	chr4:152485800-152495000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:152485800-152498800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:152486200-152489000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr4:152486400-152494800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:152487000-152488200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:152487000-152489000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:152487200-152488200	Enhancers	Fetal Intestine Small	intestine
18	chr4:152487400-152488200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:152487400-152488800	Bivalent Enhancer	GM12878-XiMat	blood
20	chr4:152487400-152489200	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr4:152487400-152489600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:152487400-152489600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:152487600-152488000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:152487800-152488400	Enhancers	Fetal Kidney	kidney

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