Variant report

Variant	rs4147137
Chromosome Location	chr9:21688238-21688239
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13287072	0.89[ASN][1000 genomes]
rs1452657	0.83[ASN][1000 genomes]
rs16938532	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16938533	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1869205	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2020334	0.84[AMR][1000 genomes]
rs2020344	0.84[AMR][1000 genomes]
rs2083560	0.86[AMR][1000 genomes]
rs2383201	0.87[CHB][hapmap];0.83[MEX][hapmap];0.84[AMR][1000 genomes]
rs28681140	0.83[ASN][1000 genomes]
rs2891163	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34410759	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs41517746	0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs4629957	0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67479509	0.93[ASN][1000 genomes]
rs7021741	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7028436	0.88[AMR][1000 genomes]
rs7028637	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7028950	0.85[AMR][1000 genomes]
rs7029077	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7035252	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7042962	0.83[ASN][1000 genomes]
rs7045371	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852691	0.86[AMR][1000 genomes]
rs7858072	0.83[ASN][1000 genomes]
rs7860632	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7865123	0.94[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7865502	0.83[ASN][1000 genomes]
rs7866337	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7866521	0.82[AMR][1000 genomes]
rs7874607	0.83[ASN][1000 genomes]
rs921560	0.87[CHB][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029634	chr9:21542970-21765286	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015623	chr9:21579110-21694039	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv892742	chr9:21589041-21707372	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv892743	chr9:21675545-21772064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4147137	FAM154A	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21680400-21691000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:21684600-21688400	Enhancers	NHLF	lung
3	chr9:21685200-21691000	Enhancers	Hela-S3	cervix
4	chr9:21685200-21695600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:21685400-21688400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:21685800-21690200	Enhancers	HUVEC	blood vessel
7	chr9:21686000-21691000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:21687200-21689400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr9:21687200-21689800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr9:21687400-21688400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:21687800-21688800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr9:21688000-21688400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr9:21688000-21688400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:21688000-21688400	Enhancers	Small Intestine	intestine
15	chr9:21688000-21688400	Flanking Active TSS	Stomach Mucosa	stomach
16	chr9:21688000-21688400	Flanking Active TSS	HSMM	muscle
17	chr9:21688000-21688400	Flanking Active TSS	NHDF-Ad	bronchial
18	chr9:21688000-21688600	Active TSS	Brain Cingulate Gyrus	brain
19	chr9:21688000-21688600	Active TSS	Brain Hippocampus Middle	brain
20	chr9:21688000-21688600	Active TSS	Brain Substantia Nigra	brain
21	chr9:21688000-21688600	Active TSS	Right Atrium	heart
22	chr9:21688000-21688800	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr9:21688000-21689600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:21688000-21689800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:21688200-21688400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:21688200-21688400	Flanking Active TSS	Colon Smooth Muscle	Colon
27	chr9:21688200-21688600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:21688200-21688600	Active TSS	Brain Angular Gyrus	brain
29	chr9:21688200-21688600	Active TSS	Brain Anterior Caudate	brain
30	chr9:21688200-21688600	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr9:21688200-21688800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:21688200-21688800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:21688200-21688800	Active TSS	Adipose Nuclei	Adipose
34	chr9:21688200-21688800	Active TSS	Duodenum Mucosa	Duodenum
35	chr9:21688200-21688800	Active TSS	A549	lung
36	chr9:21688200-21688800	Flanking Active TSS	HMEC	breast
37	chr9:21688200-21688800	Flanking Active TSS	NH-A	brain
38	chr9:21688200-21688800	Flanking Active TSS	NHEK	skin
39	chr9:21688200-21688800	Flanking Active TSS	Osteobl	bone
40	chr9:21688200-21689200	Active TSS	HSMMtube	muscle
41	chr9:21688200-21689400	Weak transcription	Esophagus	oesophagus

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