Variant report

Variant	rs8179272
Chromosome Location	chr1:78275302-78275303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1038983	0.80[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs10873951	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs10873953	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10873954	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10873955	0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11162368	0.86[AMR][1000 genomes]
rs11162370	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes]
rs11162374	0.85[AMR][1000 genomes]
rs11162378	0.95[CEU][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11162380	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs11162383	0.96[ASN][1000 genomes]
rs11162384	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11162386	0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11162387	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11578805	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1166586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1166589	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12090729	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12132838	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12135104	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12142441	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12717768	0.84[AMR][1000 genomes]
rs1389789	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs1389790	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs1539739	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs166770	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes]
rs2031342	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs203229	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2088058	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2296227	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs278832	0.89[AMR][1000 genomes]
rs278834	0.86[AMR][1000 genomes]
rs278837	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs278840	0.89[AMR][1000 genomes]
rs278841	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs278842	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs278844	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs278848	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes]
rs278850	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs278851	0.85[AMR][1000 genomes]
rs278855	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes]
rs278856	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes]
rs278858	0.80[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs278859	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs278860	0.85[CHD][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs278863	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes]
rs278864	0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs370335	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3767037	1.00[CEU][hapmap];0.84[CHD][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3767038	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4488068	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4949817	0.85[AMR][1000 genomes]
rs4949818	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs4949822	0.97[ASN][1000 genomes]
rs56688304	0.82[ASN][1000 genomes]
rs574973	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs6603956	0.80[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs6603958	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6603960	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6657290	0.80[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs6661656	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs6672200	0.80[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6687501	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6687596	0.82[ASN][1000 genomes]
rs6699205	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes]
rs6699311	0.90[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs717333	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7519946	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7535781	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7536206	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7543037	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7543125	0.97[ASN][1000 genomes]
rs7546365	0.84[AMR][1000 genomes]
rs7556227	0.97[ASN][1000 genomes]
rs7556523	0.86[AMR][1000 genomes]
rs872342	0.84[AMR][1000 genomes]
rs9662527	0.84[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs9988619	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8179272	DNAJB4	cis	parietal	SCAN
rs8179272	PIGK	cis	parietal	SCAN
rs8179272	AK5	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78246000-78284200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:78246000-78285600	Weak transcription	Colonic Mucosa	Colon
3	chr1:78246200-78279400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:78246200-78279600	Weak transcription	Aorta	Aorta
5	chr1:78246400-78287400	Weak transcription	Fetal Heart	heart
6	chr1:78247400-78278400	Weak transcription	Hela-S3	cervix
7	chr1:78248600-78288200	Weak transcription	Small Intestine	intestine
8	chr1:78250400-78282400	Weak transcription	NHEK	skin
9	chr1:78250600-78279000	Weak transcription	NHLF	lung
10	chr1:78252200-78282600	Weak transcription	Right Ventricle	heart
11	chr1:78252200-78315800	Weak transcription	Esophagus	oesophagus
12	chr1:78253000-78279400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:78253000-78283800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:78254400-78287200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:78260000-78275400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:78260600-78279800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:78262800-78285200	Weak transcription	Gastric	stomach
18	chr1:78266000-78298000	Weak transcription	K562	blood
19	chr1:78266200-78275400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:78266200-78299200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:78266200-78299200	Weak transcription	Pancreas	Pancrea
22	chr1:78266400-78279400	Weak transcription	Brain Angular Gyrus	brain
23	chr1:78266600-78284200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:78267200-78279400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:78267600-78275400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:78267800-78275400	Strong transcription	Placenta	Placenta
27	chr1:78268400-78291200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:78270200-78279200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:78271200-78275400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:78271400-78275400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr1:78271400-78275600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:78272000-78275400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:78272000-78275400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:78272400-78286200	Weak transcription	Stomach Mucosa	stomach
35	chr1:78272800-78275400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:78273400-78279400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:78273400-78279600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:78273400-78289600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:78273600-78279600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:78273600-78290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:78273600-78290000	Weak transcription	Psoas Muscle	Psoas
42	chr1:78273600-78293200	Weak transcription	Brain Germinal Matrix	brain
43	chr1:78273800-78277400	Weak transcription	Fetal Intestine Small	intestine
44	chr1:78273800-78277400	Weak transcription	Fetal Stomach	stomach
45	chr1:78273800-78279600	Weak transcription	Lung	lung
46	chr1:78273800-78284000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:78273800-78284200	Weak transcription	Spleen	Spleen
48	chr1:78274000-78279600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:78274400-78279600	Weak transcription	NH-A	brain
50	chr1:78274600-78278600	Weak transcription	Left Ventricle	heart

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