Variant report

Variant	rs12647909
Chromosome Location	chr4:76626383-76626384
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10004891	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10020040	0.85[ASN][1000 genomes]
rs10856855	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10856857	0.85[AMR][1000 genomes]
rs11097050	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11097051	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11729983	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11731107	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11731569	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12233785	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13103092	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13124724	0.86[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs13134512	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13135568	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13148199	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13152407	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17280938	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs2055998	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2137429	1.00[ASW][hapmap];0.93[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28693963	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28709419	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35443067	0.82[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap]
rs3796479	0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs4859966	0.87[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap]
rs7665811	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9306994	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9306995	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9994998	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12647909	FAM47E	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76599200-76640000	Weak transcription	Aorta	Aorta
2	chr4:76599600-76639800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:76599600-76639800	Weak transcription	Brain Angular Gyrus	brain
4	chr4:76599600-76639800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:76599600-76647600	Weak transcription	Fetal Brain Female	brain
6	chr4:76599800-76627800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:76600400-76640000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:76600600-76627000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:76605800-76633200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:76607400-76640600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:76613200-76627800	Weak transcription	A549	lung
12	chr4:76613800-76639000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:76613800-76639600	Weak transcription	Ovary	ovary
14	chr4:76614600-76630200	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:76614800-76628200	Weak transcription	Gastric	stomach
16	chr4:76615600-76639800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:76615600-76639800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:76615800-76639000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:76616000-76640000	Weak transcription	Lung	lung
20	chr4:76616200-76630200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:76618200-76635000	Weak transcription	Adipose Nuclei	Adipose
22	chr4:76618400-76639000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:76619400-76633400	Weak transcription	Fetal Kidney	kidney
24	chr4:76619600-76630400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:76620000-76630400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:76620000-76640000	Weak transcription	Brain Germinal Matrix	brain
27	chr4:76620200-76627600	Weak transcription	Liver	Liver
28	chr4:76620200-76627800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:76620200-76627800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:76620400-76627800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:76620400-76630400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:76620400-76630600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:76620400-76639600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:76620600-76627600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:76620600-76627800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr4:76620600-76627800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:76620600-76628000	Weak transcription	Fetal Stomach	stomach
38	chr4:76620600-76631400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr4:76620600-76640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:76620800-76630400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:76621000-76640600	Weak transcription	Right Ventricle	heart
42	chr4:76621800-76627800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:76621800-76642400	Weak transcription	Left Ventricle	heart
44	chr4:76622000-76627000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:76622000-76627000	Weak transcription	HepG2	liver
46	chr4:76622000-76627400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:76622000-76627800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:76622000-76627800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr4:76622000-76639400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:76622200-76626400	Weak transcription	Fetal Intestine Large	intestine

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