Variant report

Variant	rs11726647
Chromosome Location	chr4:15598478-15598479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10009089	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10034315	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11722757	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11723478	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12642407	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12650529	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13106528	0.86[JPT][hapmap]
rs13131119	0.86[JPT][hapmap]
rs13141724	0.82[JPT][hapmap]
rs13144428	0.86[JPT][hapmap]
rs13150957	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1468735	0.86[JPT][hapmap];0.83[MKK][hapmap]
rs16892135	0.86[JPT][hapmap]
rs16892143	0.86[JPT][hapmap]
rs17476670	0.86[JPT][hapmap]
rs1786	0.95[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2041672	0.86[JPT][hapmap]
rs2041673	0.86[JPT][hapmap]
rs28402170	0.91[ASN][1000 genomes]
rs28447067	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28644177	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28820655	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34473224	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34559117	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34831330	0.86[JPT][hapmap]
rs34955342	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35013326	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35120298	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756247	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3775957	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41417147	0.86[JPT][hapmap]
rs4257653	0.89[ASN][1000 genomes]
rs4267734	0.86[JPT][hapmap]
rs4301111	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4326008	0.86[JPT][hapmap]
rs4331772	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4346644	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4396986	0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4423870	0.95[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4484296	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4549375	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4600905	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4698116	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6414764	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6449150	0.86[JPT][hapmap]
rs6815254	0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6816982	0.91[ASN][1000 genomes]
rs6823775	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6824422	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6825051	0.86[JPT][hapmap]
rs6825815	0.86[JPT][hapmap]
rs6826058	0.95[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6828776	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6835038	0.86[JPT][hapmap]
rs6839654	0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6843740	0.91[ASN][1000 genomes]
rs6844141	0.86[JPT][hapmap]
rs6852735	0.93[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6857442	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7667175	0.91[ASN][1000 genomes]
rs7698596	0.91[ASN][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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11726647	LOC285550	cis	uninvolved skin	skin_eQTL
rs11726647	LOC285550	cis	multi-tissue	Pritchard
rs11726647	LOC285550	cis	lesional skin	skin_eQTL
rs11726647	FAM200B	cis	cerebellum	SCAN
rs11726647	HSP90AB2P	cis	parietal	SCAN
rs11726647	LOC285550	cis	normal skin	skin_eQTL
rs11726647	BST1	cis	multi-tissue	Pritchard
rs11726647	FAM200B	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
2	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
3	chr4:15554600-15601400	Weak transcription	A549	lung
4	chr4:15556000-15603200	Weak transcription	Fetal Thymus	thymus
5	chr4:15564000-15600600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:15564400-15603200	Weak transcription	HMEC	breast
7	chr4:15564600-15603600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:15565400-15612600	Weak transcription	Brain Substantia Nigra	brain
9	chr4:15565400-15621400	Weak transcription	Esophagus	oesophagus
10	chr4:15565600-15604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:15565600-15611400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:15565800-15605000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:15568400-15655600	Weak transcription	Gastric	stomach
14	chr4:15569600-15603600	Weak transcription	Spleen	Spleen
15	chr4:15569600-15604200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:15570200-15601800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:15570600-15602000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:15570600-15602000	Weak transcription	Pancreas	Pancrea
19	chr4:15572200-15601200	Weak transcription	NHLF	lung
20	chr4:15572200-15601800	Weak transcription	Brain Angular Gyrus	brain
21	chr4:15572200-15601800	Weak transcription	NHEK	skin
22	chr4:15572200-15604000	Weak transcription	Primary T cells from cord blood	blood
23	chr4:15572200-15604200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:15573200-15603800	Weak transcription	Fetal Intestine Small	intestine
25	chr4:15575200-15618000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:15577800-15599000	Weak transcription	Left Ventricle	heart
27	chr4:15577800-15602800	Weak transcription	Placenta	Placenta
28	chr4:15578000-15599000	Weak transcription	Aorta	Aorta
29	chr4:15579000-15599200	Weak transcription	Osteobl	bone
30	chr4:15579200-15598600	Weak transcription	Liver	Liver
31	chr4:15580400-15600000	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:15583400-15599200	Weak transcription	NH-A	brain
33	chr4:15586400-15599000	Weak transcription	Brain Anterior Caudate	brain
34	chr4:15587200-15612600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:15588200-15601200	Weak transcription	Primary B cells from cord blood	blood
36	chr4:15589000-15600000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr4:15589200-15602800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:15589600-15602000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:15589600-15603000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:15589800-15599000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:15589800-15621400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:15590000-15603200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:15590000-15615600	Weak transcription	Lung	lung
44	chr4:15590200-15598600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:15590400-15604200	Weak transcription	Fetal Intestine Large	intestine
46	chr4:15590600-15598600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr4:15590600-15626400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr4:15593800-15604200	Weak transcription	Brain Germinal Matrix	brain
49	chr4:15593800-15621200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr4:15594000-15601400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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