Variant report

Variant	rs4261975
Chromosome Location	chr4:120025002-120025003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs17050059	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs17272604	0.86[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17332199	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1903108	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1982571	0.87[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4240323	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4320121	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4320122	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4374608	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4407485	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4420962	0.87[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4420963	0.87[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4440202	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4508865	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4565063	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4572857	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4629433	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4637382	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4834747	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4834748	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5008976	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5008977	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6813730	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6819075	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6845990	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6851886	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6852072	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6852315	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7669848	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1007214	chr4:120007913-120112460	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv1003827	chr4:120008227-120112460	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv522386	chr4:120009147-120115379	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
9	nsv1007619	chr4:120014898-120112460	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4261975	KIAA1109	cis	cerebellum	SCAN
rs4261975	USP53	cis	lung	GTEx
rs4261975	MDGA2	trans	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120014800-120045000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:120015000-120027800	Weak transcription	Right Atrium	heart
3	chr4:120017000-120027600	Weak transcription	Left Ventricle	heart
4	chr4:120021600-120026400	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr4:120022200-120027800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:120022400-120025200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:120022800-120028200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:120022800-120028200	Enhancers	NHEK	skin
9	chr4:120023000-120026400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:120023000-120028200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:120023200-120025400	Enhancers	NH-A	brain
12	chr4:120023200-120025600	Enhancers	NHLF	lung
13	chr4:120023200-120026200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:120023200-120028200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr4:120023200-120028600	Enhancers	HUVEC	blood vessel
16	chr4:120023200-120029400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:120023400-120026200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:120023600-120025200	Flanking Active TSS	A549	lung
19	chr4:120023600-120026200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr4:120023600-120028200	Enhancers	Hela-S3	cervix
21	chr4:120023800-120025200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:120023800-120026200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr4:120023800-120026400	Enhancers	HSMMtube	muscle
24	chr4:120023800-120026400	Enhancers	NHDF-Ad	bronchial
25	chr4:120023800-120027800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:120023800-120028000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:120023800-120028200	Enhancers	HSMM	muscle
28	chr4:120024000-120025200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr4:120024000-120027800	Enhancers	Osteobl	bone
30	chr4:120024200-120025200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:120024400-120025200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr4:120024400-120025200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:120024400-120025200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr4:120024400-120025600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr4:120024600-120025200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr4:120024600-120026000	Weak transcription	Psoas Muscle	Psoas
37	chr4:120024600-120027200	Weak transcription	Fetal Muscle Leg	muscle
38	chr4:120024600-120027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:120024600-120027400	Weak transcription	Placenta	Placenta
40	chr4:120024600-120036800	Weak transcription	Right Ventricle	heart
41	chr4:120024800-120025200	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr4:120024800-120026200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:120025000-120025200	Enhancers	Colon Smooth Muscle	Colon
44	chr4:120025000-120026000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:120025000-120026600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr4:120025000-120027000	Weak transcription	Adipose Nuclei	Adipose
47	chr4:120025000-120027200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:120025000-120027200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr4:120025000-120027200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:120025000-120027800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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