Variant report

Variant	rs1946999
Chromosome Location	chr4:152455339-152455340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11726254	0.81[ASN][1000 genomes]
rs12647555	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs1372976	0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1372977	0.83[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs1372978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443087	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1443088	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1443089	0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1443090	0.84[ASN][1000 genomes]
rs1443094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470280	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap]
rs1561915	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1561918	0.81[ASN][1000 genomes]
rs2053566	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2709816	0.81[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2709826	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap]
rs2709828	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap]
rs2709831	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2709832	0.82[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap]
rs2724567	0.82[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap]
rs2724568	0.82[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs2724577	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs3919716	0.85[EUR][1000 genomes]
rs3929153	0.81[ASN][1000 genomes]
rs4263379	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4696099	0.86[GIH][hapmap]
rs55668815	0.86[EUR][1000 genomes]
rs56301462	0.84[ASN][1000 genomes]
rs6814554	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6825241	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6826799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73862064	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7666571	0.81[ASN][1000 genomes]
rs7695162	0.80[EUR][1000 genomes]
rs7695412	0.86[GIH][hapmap]

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	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1025192	chr4:152202627-152498890	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537307	chr4:152202627-152498890	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv881342	chr4:152363772-152560449	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv830114	chr4:152401288-152548606	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv508321	chr4:152409994-152474456	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1946999	PET112L	cis	cerebellum	SCAN
rs1946999	SH3D19	cis	cerebellum	SCAN
rs1946999	PET112L	cis	parietal	SCAN
rs1946999	PET112L	cis	lymphoblastoid	seeQTL
rs1946999	FAM160A1	cis	Whole Blood	GTEx
rs1946999	FAM160A1	cis	cerebellum	SCAN
rs1946999	FAM160A1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152444200-152459200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:152445800-152461400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:152445800-152468200	Weak transcription	Esophagus	oesophagus
4	chr4:152446800-152458800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:152446800-152458800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr4:152446800-152459000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:152446800-152462200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:152447000-152458800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:152448800-152458200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr4:152449000-152461400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:152449400-152462600	Weak transcription	Pancreas	Pancrea
12	chr4:152451800-152460800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:152452000-152456800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:152452000-152458800	Weak transcription	NHEK	skin
15	chr4:152452000-152459000	Weak transcription	HMEC	breast
16	chr4:152452000-152468200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:152452800-152457200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:152453400-152456200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:152453800-152458600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:152453800-152458800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:152454000-152458800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:152454000-152468000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:152454200-152456000	Weak transcription	Psoas Muscle	Psoas
24	chr4:152454200-152456400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr4:152454800-152457200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr4:152455200-152455600	Enhancers	Fetal Heart	heart

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