Variant report

Variant	rs10873955
Chromosome Location	chr1:78284211-78284212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1038983	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10873954	0.96[ASN][1000 genomes]
rs11162366	0.81[EUR][1000 genomes]
rs11162378	0.83[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs11162380	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11162383	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162384	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162386	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162387	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578805	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1166584	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1166586	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1166588	0.80[TSI][hapmap]
rs1166589	0.97[ASN][1000 genomes]
rs12026939	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12090729	1.00[ASN][1000 genomes]
rs12132838	0.80[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12142441	0.80[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12142671	0.94[CEU][hapmap];0.80[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs1389789	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs1389790	0.80[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs1539739	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs166770	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1977900	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2031342	0.80[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs203229	0.80[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs2147318	0.94[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2274123	0.80[TSI][hapmap]
rs2296227	0.80[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap]
rs278833	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278836	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278837	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs278842	0.80[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs278843	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278848	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs278850	0.80[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs278854	0.94[CEU][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs278855	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs278856	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs278857	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278858	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278859	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278860	0.83[CEU][hapmap];0.88[CHD][hapmap]
rs278863	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs278864	0.94[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs366467	0.85[EUR][1000 genomes]
rs370335	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs371076	0.94[CEU][hapmap];0.80[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs3767037	0.80[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap]
rs3767038	0.80[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4488068	0.86[ASN][1000 genomes]
rs4949661	0.82[EUR][1000 genomes]
rs4949814	0.81[EUR][1000 genomes]
rs4949822	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56688304	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs574973	0.80[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs6603956	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6603958	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs6603960	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs6657290	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6661656	0.80[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs6670660	0.82[EUR][1000 genomes]
rs6672200	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6674638	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6687501	0.80[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs6687596	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6691317	0.82[EUR][1000 genomes]
rs6698151	0.82[EUR][1000 genomes]
rs6699205	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs6699311	0.90[JPT][hapmap]
rs717333	0.80[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7519946	0.84[ASN][1000 genomes]
rs7535781	0.80[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7536206	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543037	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7543125	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545175	0.82[EUR][1000 genomes]
rs7556227	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8179272	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]
rs9662527	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][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
rs10873955	AK5	cis	parietal	SCAN
rs10873955	DNAJB4	cis	parietal	SCAN
rs10873955	PIGK	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78246000-78285600	Weak transcription	Colonic Mucosa	Colon
2	chr1:78246400-78287400	Weak transcription	Fetal Heart	heart
3	chr1:78248600-78288200	Weak transcription	Small Intestine	intestine
4	chr1:78252200-78315800	Weak transcription	Esophagus	oesophagus
5	chr1:78254400-78287200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:78262800-78285200	Weak transcription	Gastric	stomach
7	chr1:78266000-78298000	Weak transcription	K562	blood
8	chr1:78266200-78299200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:78266200-78299200	Weak transcription	Pancreas	Pancrea
10	chr1:78268400-78291200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:78272400-78286200	Weak transcription	Stomach Mucosa	stomach
12	chr1:78273400-78289600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:78273600-78290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:78273600-78290000	Weak transcription	Psoas Muscle	Psoas
15	chr1:78273600-78293200	Weak transcription	Brain Germinal Matrix	brain
16	chr1:78274600-78288600	Weak transcription	HepG2	liver
17	chr1:78274600-78290800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:78274800-78297400	Weak transcription	Brain Substantia Nigra	brain
19	chr1:78274800-78297600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:78274800-78298000	Weak transcription	Fetal Kidney	kidney
21	chr1:78275000-78289000	Weak transcription	A549	lung
22	chr1:78275000-78312800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:78277000-78290200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:78277400-78291200	Strong transcription	Fetal Intestine Small	intestine
25	chr1:78277600-78292600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr1:78278400-78284400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:78278400-78286200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:78278400-78286400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:78278400-78289600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr1:78278600-78286400	Strong transcription	Primary T cells from cord blood	blood
31	chr1:78278600-78287000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:78278800-78287400	Strong transcription	Placenta	Placenta
33	chr1:78278800-78288800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:78278800-78290200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:78279200-78286600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:78279200-78288000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:78279200-78288000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:78279200-78288200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:78279200-78288200	Strong transcription	Liver	Liver
40	chr1:78279200-78288400	Strong transcription	Fetal Intestine Large	intestine
41	chr1:78279200-78288800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr1:78279200-78289600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:78279200-78300400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:78279400-78284400	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:78279400-78284400	Strong transcription	HUVEC	blood vessel
46	chr1:78279400-78285600	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:78279400-78286600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:78279400-78289600	Strong transcription	Fetal Thymus	thymus
49	chr1:78279400-78289800	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr1:78279400-78290600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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