Variant report

Variant	rs6859562
Chromosome Location	chr5:112402998-112402999
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112402187..112405327-chr5:112405857..112410029,4	K562	blood:
2	chr5:112398620..112400244-chr5:112402557..112404477,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10036854	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10039618	0.84[CHB][hapmap]
rs10045658	0.84[CHB][hapmap]
rs10058407	0.81[CHB][hapmap]
rs10077067	0.90[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10223151	0.84[CHB][hapmap]
rs10223152	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs11241190	0.84[CHB][hapmap]
rs11744218	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs11744817	0.90[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11744828	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs11744956	0.84[CHB][hapmap]
rs11750093	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs11960706	0.81[JPT][hapmap]
rs28535973	0.91[ASN][1000 genomes]
rs28620751	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3890775	0.84[CHB][hapmap]
rs4283779	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs4397121	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs4645326	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs4705539	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs4705758	0.84[CHB][hapmap]
rs6594672	0.80[ASN][1000 genomes]
rs6594673	0.80[ASN][1000 genomes]
rs6594680	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs6859485	0.88[CEU][hapmap]
rs6861166	0.84[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs6861336	0.90[CEU][hapmap]
rs6862481	0.89[CHB][hapmap]
rs6865585	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6865804	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6866566	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs6866706	0.82[CHB][hapmap]
rs6873623	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs6874727	0.82[ASN][1000 genomes]
rs6879138	0.84[CHB][hapmap]
rs6879589	0.82[CHB][hapmap]
rs6879633	0.89[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs6879942	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs6882155	0.90[CEU][hapmap]
rs6882309	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6888031	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6888485	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6890833	1.00[CEU][hapmap]
rs6898297	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs7713290	0.83[CHB][hapmap]
rs7713336	0.84[CHB][hapmap]
rs7714010	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs7714160	0.84[CHB][hapmap]
rs7714492	0.84[CHB][hapmap]
rs7714725	0.84[CHB][hapmap]
rs7734411	0.84[CHB][hapmap]
rs7736823	0.84[CHB][hapmap]
rs9326874	0.84[CHB][hapmap]
rs9326875	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv15902	chr5:112369563-112410775	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599395	chr5:112370311-112428869	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1032798	chr5:112392380-112408177	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6859562	AQPEP	cis	parietal	SCAN
rs6859562	MCC	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112363800-112409200	Weak transcription	Colonic Mucosa	Colon
2	chr5:112363800-112417800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr5:112370200-112406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:112371400-112423800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:112379600-112424200	Weak transcription	Psoas Muscle	Psoas
6	chr5:112383200-112409400	Strong transcription	Liver	Liver
7	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:112384200-112411000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:112390800-112410800	Weak transcription	Fetal Intestine Small	intestine
10	chr5:112391600-112439000	Weak transcription	Gastric	stomach
11	chr5:112395000-112411600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:112395600-112403400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:112395600-112403600	Weak transcription	Fetal Brain Male	brain
14	chr5:112395600-112417600	Weak transcription	Brain Angular Gyrus	brain
15	chr5:112395600-112420400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:112395800-112408600	Weak transcription	Brain Anterior Caudate	brain
17	chr5:112395800-112409000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:112396000-112417200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:112396800-112404600	Genic enhancers	Fetal Stomach	stomach
20	chr5:112397400-112405000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:112397800-112403800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:112398400-112403400	Strong transcription	Stomach Smooth Muscle	stomach
23	chr5:112398400-112404600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:112398400-112407400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:112398600-112407000	Strong transcription	NHEK	skin
26	chr5:112398600-112409800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:112398800-112412400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:112399000-112404600	Weak transcription	Fetal Heart	heart
29	chr5:112399000-112405200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:112399000-112406000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:112399000-112406800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:112399000-112432800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:112399200-112417600	Weak transcription	Fetal Kidney	kidney
34	chr5:112399400-112404000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:112399600-112405800	Weak transcription	HUVEC	blood vessel
36	chr5:112399800-112403400	Weak transcription	Brain Substantia Nigra	brain
37	chr5:112399800-112405000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr5:112399800-112406200	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:112399800-112408400	Weak transcription	Right Atrium	heart
40	chr5:112399800-112441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:112400000-112403600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr5:112400000-112417600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr5:112400200-112403000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:112400200-112403600	Weak transcription	Brain Hippocampus Middle	brain
45	chr5:112400200-112411400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:112400200-112416800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:112400200-112416800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr5:112400400-112403200	Enhancers	HSMMtube	muscle
49	chr5:112400400-112403800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:112400400-112404600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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