Variant report

Variant	rs3756247
Chromosome Location	chr4:15706466-15706467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10009089	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10017222	1.00[CHB][hapmap]
rs10034315	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10516289	1.00[CHB][hapmap]
rs11722757	0.98[ASN][1000 genomes]
rs11722854	0.81[ASN][1000 genomes]
rs11723478	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11723554	1.00[CHB][hapmap]
rs11726647	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11729955	1.00[CHB][hapmap]
rs11735063	0.86[CHB][hapmap]
rs12642407	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650529	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13106528	0.88[JPT][hapmap]
rs13131119	0.86[JPT][hapmap]
rs13141724	0.85[JPT][hapmap]
rs13144428	0.86[JPT][hapmap]
rs13150957	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1468735	0.86[JPT][hapmap]
rs1468736	0.82[JPT][hapmap]
rs16892135	0.86[JPT][hapmap]
rs16892143	0.86[JPT][hapmap]
rs16892156	0.82[JPT][hapmap]
rs17405811	1.00[CHB][hapmap]
rs17476642	1.00[CHB][hapmap]
rs17476670	0.86[JPT][hapmap]
rs1786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2041672	0.86[JPT][hapmap]
rs2041673	0.86[JPT][hapmap]
rs28394730	0.81[ASN][1000 genomes]
rs28402170	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28447067	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28604503	0.81[ASN][1000 genomes]
rs28644177	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28820655	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34473224	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34559117	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34831330	0.86[JPT][hapmap]
rs34955342	0.98[ASN][1000 genomes]
rs35013326	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35120298	0.96[ASN][1000 genomes]
rs3775957	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs41417147	0.86[JPT][hapmap]
rs4257653	0.98[ASN][1000 genomes]
rs4267734	0.86[JPT][hapmap]
rs4301111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4326008	0.86[JPT][hapmap]
rs4331772	0.98[ASN][1000 genomes]
rs4346644	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4396986	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423870	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4484296	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4554069	0.81[ASN][1000 genomes]
rs4600905	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4698116	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6414764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6449150	0.86[JPT][hapmap]
rs6815254	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815296	1.00[CHB][hapmap]
rs6816982	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823775	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6824422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6825051	0.88[JPT][hapmap]
rs6825815	0.86[JPT][hapmap]
rs6826058	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6827406	1.00[CHB][hapmap]
rs6828776	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6839654	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843740	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848779	1.00[CHB][hapmap]
rs6852735	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6857442	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7434484	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7667175	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698596	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9994518	0.85[CHB][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
6	esv3345585	chr4:15704254-15707452	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3414958	chr4:15704254-15708452	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv20430	chr4:15705044-15706579	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3756247	LOC285550	cis	normal skin	skin_eQTL
rs3756247	LOC285550	cis	uninvolved skin	skin_eQTL
rs3756247	LOC285550	cis	lesional skin	skin_eQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15697600-15723600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:15703200-15706600	Weak transcription	HepG2	liver
3	chr4:15704600-15708200	Weak transcription	Fetal Heart	heart
4	chr4:15705000-15708400	Weak transcription	HSMMtube	muscle
5	chr4:15705000-15708600	Weak transcription	Liver	Liver
6	chr4:15705000-15708600	Weak transcription	Fetal Brain Female	brain
7	chr4:15705000-15735200	Weak transcription	Lung	lung
8	chr4:15705200-15706600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:15705200-15706600	Weak transcription	Brain Substantia Nigra	brain
10	chr4:15705200-15708200	Weak transcription	NHDF-Ad	bronchial
11	chr4:15705200-15708400	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:15705200-15708400	Weak transcription	Ovary	ovary
13	chr4:15705200-15716200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:15705200-15716200	Weak transcription	Brain Anterior Caudate	brain
15	chr4:15705200-15720400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:15705200-15720600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:15705200-15731000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:15705400-15707200	Weak transcription	Fetal Kidney	kidney
19	chr4:15705400-15707600	Weak transcription	Adipose Nuclei	Adipose
20	chr4:15705400-15708800	Weak transcription	Brain Angular Gyrus	brain
21	chr4:15705400-15708800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:15705400-15709200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:15705400-15709600	Weak transcription	Fetal Intestine Small	intestine
24	chr4:15705400-15713800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:15705400-15715800	Weak transcription	Fetal Lung	lung
26	chr4:15705400-15715800	Weak transcription	Fetal Stomach	stomach
27	chr4:15705400-15715800	Weak transcription	NH-A	brain
28	chr4:15705400-15716200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:15705400-15716200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:15705400-15716200	Weak transcription	A549	lung
31	chr4:15705400-15718800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:15705400-15727400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:15705600-15707800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:15705600-15708400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:15705600-15714000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:15705800-15706600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr4:15705800-15708000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:15705800-15715600	Weak transcription	Osteobl	bone
39	chr4:15705800-15716200	Weak transcription	Fetal Intestine Large	intestine
40	chr4:15705800-15719400	Weak transcription	Spleen	Spleen
41	chr4:15706000-15727800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr4:15706200-15706800	Weak transcription	Primary B cells from cord blood	blood
43	chr4:15706200-15706800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
44	chr4:15706400-15707400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood

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