Variant report

Variant	rs41464847
Chromosome Location	chr4:120532401-120532402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120532371..120535379-chr4:120540193..120542602,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10518329	0.87[CHB][hapmap];0.84[CHD][hapmap]
rs10518336	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]
rs10518337	0.84[EUR][1000 genomes]
rs1155577	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12512646	0.83[JPT][hapmap]
rs12648182	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13104219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13134517	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1480933	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs2389873	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2389875	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2622503	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2715016	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2892869	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36173322	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3775842	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4833624	0.83[JPT][hapmap]
rs4834792	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55661135	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56173225	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56843000	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59516282	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59590064	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66887589	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6817317	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6843229	0.87[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs6844263	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs72920701	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7665125	0.87[CHB][hapmap]
rs7672519	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7678973	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7681980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7692994	0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs41464847	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs41464847	TRPC3	cis	parietal	SCAN
rs41464847	C4orf3	cis	cerebellum	SCAN
rs41464847	USP53	cis	parietal	SCAN
rs41464847	LOC645513	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
3	chr4:120517000-120536600	Weak transcription	Ovary	ovary
4	chr4:120518800-120547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:120519000-120533400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:120520200-120536400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:120520400-120533200	Weak transcription	Fetal Intestine Small	intestine
8	chr4:120520400-120537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr4:120521000-120544800	Weak transcription	Fetal Intestine Large	intestine
10	chr4:120525800-120538800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:120526200-120546800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:120526400-120544200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:120526600-120532600	Weak transcription	Fetal Lung	lung
14	chr4:120526600-120535400	Weak transcription	Fetal Brain Male	brain
15	chr4:120527400-120536400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:120528400-120532600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:120528400-120547400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:120528600-120532600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:120528600-120533200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:120528600-120533400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:120528600-120547400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:120528600-120547600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:120528800-120533800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:120528800-120539000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:120528800-120540200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:120528800-120543000	Weak transcription	Pancreas	Pancrea
27	chr4:120528800-120544200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr4:120528800-120545400	Weak transcription	Fetal Stomach	stomach
29	chr4:120529000-120546600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:120531600-120532800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:120531600-120534800	Strong transcription	Osteobl	bone
32	chr4:120532000-120534000	Strong transcription	NHLF	lung
33	chr4:120532000-120536200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:120532200-120533600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:120532200-120535600	Weak transcription	Colon Smooth Muscle	Colon
36	chr4:120532200-120536000	Weak transcription	Aorta	Aorta
37	chr4:120532400-120536600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:120532400-120547600	Weak transcription	Lung	lung

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