Variant report

Variant	rs12568083
Chromosome Location	chr1:154455949-154455950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10908841	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908842	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908843	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908845	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10908847	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11265621	0.96[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11265622	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265628	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265632	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12037271	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118018	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12119111	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12128408	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12136771	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12407048	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12740969	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12753666	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12753680	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4074436	0.86[LWK][hapmap]
rs4345797	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4382717	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4478801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4584384	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4638123	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845637	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845642	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845647	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5018567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6658175	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6664608	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6684921	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6686276	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689965	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7518694	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7519499	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9660786	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12568083	EFNA4	cis	parietal	SCAN
rs12568083	SHC1	cis	parietal	SCAN
rs12568083	LCE2B	cis	cerebellum	SCAN
rs12568083	CRNN	cis	cerebellum	SCAN
rs12568083	S100A3	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154427800-154464800	Weak transcription	Ovary	ovary
2	chr1:154438400-154457800	Weak transcription	Pancreas	Pancrea
3	chr1:154438400-154458400	Weak transcription	Gastric	stomach
4	chr1:154438400-154463400	Weak transcription	Esophagus	oesophagus
5	chr1:154439400-154457600	Weak transcription	Placenta	Placenta
6	chr1:154440000-154458200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:154441600-154465200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:154442800-154456400	Weak transcription	Spleen	Spleen
9	chr1:154443000-154456400	Weak transcription	Right Ventricle	heart
10	chr1:154443000-154464400	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:154447800-154458400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:154448600-154458200	Weak transcription	Brain Substantia Nigra	brain
13	chr1:154449800-154456400	Weak transcription	Hela-S3	cervix
14	chr1:154450000-154457000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:154450000-154462400	Weak transcription	Colonic Mucosa	Colon
16	chr1:154450200-154456600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:154451400-154456400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:154451400-154456600	Weak transcription	NHEK	skin
19	chr1:154451600-154465600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:154451800-154456800	Genic enhancers	HUVEC	blood vessel
21	chr1:154452400-154456600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:154452400-154457000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:154452400-154457600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:154452400-154457600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:154452400-154458200	Weak transcription	Fetal Intestine Small	intestine
26	chr1:154452600-154458200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:154452800-154456400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr1:154452800-154457600	Weak transcription	Fetal Lung	lung
29	chr1:154452800-154458000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:154452800-154458200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:154452800-154458400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:154452800-154458400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:154452800-154458400	Weak transcription	Fetal Stomach	stomach
34	chr1:154452800-154458400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:154453000-154457000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:154453000-154458200	Weak transcription	Liver	Liver
37	chr1:154453000-154458200	Weak transcription	Brain Anterior Caudate	brain
38	chr1:154453000-154458200	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:154453600-154456800	Weak transcription	A549	lung
40	chr1:154453600-154457800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:154454000-154456600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:154454000-154457800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:154454000-154457800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:154454000-154461800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:154454800-154458000	Weak transcription	Brain Germinal Matrix	brain
46	chr1:154455200-154456600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:154455200-154461600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:154455600-154456000	Strong transcription	Left Ventricle	heart
49	chr1:154455600-154456400	Strong transcription	Adipose Nuclei	Adipose
50	chr1:154455600-154460200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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