Variant report

Variant	rs10518336
Chromosome Location	chr4:120522934-120522935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10006525	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs10006706	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs10013305	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs10017335	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs10018280	0.85[CHB][hapmap]
rs10019674	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs10030660	0.86[CHB][hapmap]
rs10031483	0.86[CHB][hapmap]
rs10050092	0.84[CHB][hapmap];0.81[YRI][hapmap]
rs1010739	0.86[CHB][hapmap]
rs1010740	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs10518328	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs11098531	0.86[CHB][hapmap]
rs1155576	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs1155577	0.88[CEU][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap]
rs11723090	0.86[CHB][hapmap]
rs11729521	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs11731756	0.86[CHB][hapmap]
rs11734241	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs11737395	0.86[CHB][hapmap]
rs11933966	0.86[CHB][hapmap]
rs11935596	0.86[CHB][hapmap]
rs11947234	0.86[CHB][hapmap]
rs12498599	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs12502423	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs12505735	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs12507964	0.86[CHB][hapmap]
rs12508504	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs12510138	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs12648182	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13104219	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs13128602	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs13134517	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs13134665	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs1383532	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs1480931	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs1480933	0.88[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs1480936	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs1480940	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs1552092	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs1552095	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs17006190	0.86[CHB][hapmap]
rs17050695	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs2127823	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs2170276	0.86[CHB][hapmap]
rs2291185	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs2306456	0.86[CHB][hapmap]
rs2389803	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2389809	0.86[CHB][hapmap]
rs2622503	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28535956	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs28578366	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs2892848	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2892869	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3733519	0.89[CHB][hapmap]
rs3733524	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs3736115	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs3756156	0.90[CHB][hapmap]
rs3775843	0.81[CHB][hapmap]
rs3775844	0.86[CHB][hapmap]
rs3775845	0.86[CHB][hapmap]
rs3775848	0.81[CHB][hapmap]
rs3775852	0.86[CHB][hapmap]
rs3806808	0.91[CHB][hapmap]
rs3822192	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs3822194	0.86[CHB][hapmap]
rs3822195	0.82[CHB][hapmap]
rs41464847	0.88[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55661135	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56173225	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56843000	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59516282	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59590064	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6534139	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs66887589	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6817317	0.82[ASN][1000 genomes]
rs6832740	0.86[CHB][hapmap];0.86[CHD][hapmap];0.80[LWK][hapmap];0.80[MKK][hapmap];0.84[YRI][hapmap]
rs6834796	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs6835635	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs6843229	0.86[CHB][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap]
rs6844263	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs6848389	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs6849171	0.86[CHB][hapmap]
rs6849561	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs6853998	0.86[CHB][hapmap]
rs72920701	0.81[ASN][1000 genomes]
rs7659501	0.86[CHB][hapmap]
rs7672519	0.82[ASN][1000 genomes]
rs7678973	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7681544	0.86[CHB][hapmap]
rs7681980	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7687843	0.86[CHB][hapmap]
rs7688802	0.85[CHB][hapmap]
rs7695620	0.86[CHB][hapmap]
rs7699064	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs9884402	0.86[CHB][hapmap]
rs9997631	0.84[CHB][hapmap]
rs9998585	0.86[CHB][hapmap]

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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10518336	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs10518336	USP53	cis	parietal	SCAN
rs10518336	TRPC3	cis	parietal	SCAN
rs10518336	SYNPO2	cis	cerebellum	SCAN
rs10518336	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs10518336	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120486800-120527600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:120502200-120527800	Weak transcription	Pancreas	Pancrea
4	chr4:120502400-120526400	Weak transcription	Fetal Stomach	stomach
5	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
6	chr4:120506200-120525800	Weak transcription	Fetal Kidney	kidney
7	chr4:120512600-120530400	Weak transcription	Colonic Mucosa	Colon
8	chr4:120512800-120531600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:120514200-120528600	Weak transcription	Gastric	stomach
10	chr4:120516800-120527800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:120517000-120527600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:120517000-120527800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:120517000-120531400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:120517000-120536600	Weak transcription	Ovary	ovary
15	chr4:120518800-120524400	Weak transcription	Fetal Heart	heart
16	chr4:120518800-120547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:120519000-120533400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:120519600-120528600	Strong transcription	Osteobl	bone
19	chr4:120519800-120527600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:120519800-120527800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:120520200-120524000	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:120520200-120525000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:120520200-120525200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:120520200-120525200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:120520200-120525200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:120520200-120527800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:120520200-120527800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:120520200-120529800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr4:120520200-120536400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:120520400-120525400	Weak transcription	Small Intestine	intestine
31	chr4:120520400-120525800	Weak transcription	Psoas Muscle	Psoas
32	chr4:120520400-120533200	Weak transcription	Fetal Intestine Small	intestine
33	chr4:120520400-120537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr4:120520600-120524400	Weak transcription	Fetal Muscle Leg	muscle
35	chr4:120520600-120527800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:120520600-120529600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:120520800-120527600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:120520800-120527800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr4:120520800-120529400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:120521000-120524000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:120521000-120524600	Strong transcription	NHLF	lung
42	chr4:120521000-120529800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:120521000-120544800	Weak transcription	Fetal Intestine Large	intestine
44	chr4:120521200-120527400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr4:120521400-120527800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:120521600-120524600	Strong transcription	Fetal Lung	lung
47	chr4:120522000-120530400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:120522200-120523000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:120522200-120523000	Strong transcription	Aorta	Aorta
50	chr4:120522800-120523000	Enhancers	Lung	lung

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