Variant report

Variant	rs12143948
Chromosome Location	chr1:155509242-155509243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10752611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10796943	1.00[CHB][hapmap]
rs10796945	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs10908465	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs10908469	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10908470	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10908471	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10908479	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11264363	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs11264367	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264369	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11264371	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11264372	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11264375	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11264380	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs11264381	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11264387	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap]
rs12026638	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12035524	0.91[JPT][hapmap]
rs12041534	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12047756	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12079134	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12239114	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs12724079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap]
rs12744132	0.91[JPT][hapmap]
rs12746592	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1325908	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs1360554	1.00[ASW][hapmap];0.96[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];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1556488	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs1886905	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap]
rs2048431	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2175391	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs2666826	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs348196	0.91[JPT][hapmap]
rs35615695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs3738590	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs3892792	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs475550	0.91[JPT][hapmap];0.83[MEX][hapmap]
rs5005770	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs644853	1.00[JPT][hapmap]
rs6684889	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap]
rs6688636	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs6696888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs678157	0.91[JPT][hapmap]
rs7556102	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs821551	0.81[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][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	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv1799856	chr1:155305059-155534616	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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 miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1795662	chr1:155305059-155540660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS 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 miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv1795478	chr1:155334933-155510824	Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv1803551	chr1:155334933-155522572	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv1800974	chr1:155367680-155510824	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv872468	chr1:155413304-155549562	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12143948	PRUNE	cis	cerebellum	SCAN
rs12143948	S100A8	cis	cerebellum	SCAN
rs12143948	C1orf56	cis	parietal	SCAN
rs12143948	CRNN	cis	cerebellum	SCAN
rs12143948	YY1AP1	cis	parietal	SCAN
rs12143948	BCAN	cis	cerebellum	SCAN
rs12143948	GBAP1	cis	parietal	SCAN
rs12143948	YY1AP1	cis	cerebellum	SCAN
rs12143948	HDGF	cis	parietal	SCAN
rs12143948	THEM5	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155476400-155518200	Weak transcription	HMEC	breast
2	chr1:155477600-155509400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:155478400-155510400	Weak transcription	Stomach Mucosa	stomach
4	chr1:155478400-155518200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:155483200-155524400	Weak transcription	Fetal Brain Female	brain
6	chr1:155483400-155528600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:155488000-155513400	Weak transcription	Fetal Stomach	stomach
8	chr1:155489800-155516200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:155489800-155529400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:155490000-155513000	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:155491000-155509400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:155491200-155521800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:155491400-155523400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:155491600-155516200	Weak transcription	NHEK	skin
15	chr1:155493400-155514200	Weak transcription	Gastric	stomach
16	chr1:155496600-155518400	Weak transcription	HSMM	muscle
17	chr1:155496600-155529800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:155497800-155513600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:155498000-155513000	Weak transcription	Hela-S3	cervix
20	chr1:155499600-155517000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:155500000-155516400	Weak transcription	NHDF-Ad	bronchial
22	chr1:155500000-155524400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr1:155500200-155519800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:155501000-155511800	Weak transcription	Aorta	Aorta
25	chr1:155501800-155511200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:155501800-155523200	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:155502000-155509800	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:155502000-155509800	Weak transcription	Fetal Kidney	kidney
29	chr1:155502000-155516200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:155502000-155518000	Weak transcription	Brain Anterior Caudate	brain
31	chr1:155502000-155518800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:155503000-155512000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:155503400-155519600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:155503800-155523200	Weak transcription	Fetal Thymus	thymus
35	chr1:155504000-155512000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr1:155504200-155510000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr1:155504200-155510000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr1:155505000-155509400	Weak transcription	Lung	lung
39	chr1:155505200-155509400	Weak transcription	Pancreas	Pancrea
40	chr1:155505200-155509400	Weak transcription	Right Atrium	heart
41	chr1:155505200-155513000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:155505400-155518200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:155505600-155523400	Weak transcription	Placenta	Placenta
44	chr1:155506200-155513600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:155506400-155509400	Weak transcription	Liver	Liver
46	chr1:155506400-155510000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:155506400-155510000	Weak transcription	A549	lung
48	chr1:155506400-155510200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:155506400-155510400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:155506400-155523400	Weak transcription	Primary hematopoietic stem cells	blood

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