Variant report

Variant	rs1279840
Chromosome Location	chr3:136006576-136006577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10935177	0.86[JPT][hapmap]
rs10935182	0.93[JPT][hapmap]
rs10935183	0.87[JPT][hapmap]
rs10935184	1.00[JPT][hapmap]
rs1145101	0.88[MEX][hapmap]
rs1145106	0.90[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs1153871	0.82[ASN][1000 genomes]
rs1153877	1.00[JPT][hapmap]
rs1154988	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.87[MKK][hapmap];0.85[YRI][hapmap]
rs11715257	0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs11717954	0.87[JPT][hapmap]
rs12330635	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12492510	0.87[JPT][hapmap]
rs1278493	0.86[JPT][hapmap]
rs1278719	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1279086	1.00[JPT][hapmap]
rs1279425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1279831	0.86[JPT][hapmap]
rs1291921	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13068119	0.83[MEX][hapmap]
rs1394092	0.80[ASW][hapmap];0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap]
rs1618069	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1711161	0.90[CEU][hapmap];0.87[JPT][hapmap]
rs1711170	0.86[JPT][hapmap]
rs1711171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17252498	0.83[MEX][hapmap]
rs2655008	0.93[JPT][hapmap]
rs3755636	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3772390	0.88[CHB][hapmap]
rs3821445	0.84[CEU][hapmap];0.88[MEX][hapmap]
rs3957816	0.86[JPT][hapmap]
rs4678428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs483465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518972	1.00[JPT][hapmap]
rs521746	0.87[JPT][hapmap]
rs523118	0.81[EUR][1000 genomes]
rs534944	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs548288	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs553018	0.93[JPT][hapmap]
rs556788	1.00[JPT][hapmap]
rs571513	0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs576771	1.00[CEU][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs589092	1.00[JPT][hapmap]
rs595532	0.93[JPT][hapmap]
rs606725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs610860	0.84[CEU][hapmap]
rs619605	0.93[JPT][hapmap]
rs632016	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs645040	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs650326	1.00[JPT][hapmap]
rs650505	0.96[ASN][1000 genomes]
rs654237	0.93[JPT][hapmap]
rs655720	0.82[ASN][1000 genomes]
rs655836	0.93[JPT][hapmap]
rs661739	0.86[JPT][hapmap]
rs665200	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs667920	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6770476	0.83[ASN][1000 genomes]
rs6789488	0.80[EUR][1000 genomes]
rs6791611	0.87[JPT][hapmap]
rs684773	0.84[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs687339	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap]
rs695983	0.89[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.87[ASN][1000 genomes]
rs696081	1.00[JPT][hapmap]
rs696516	0.85[CEU][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs696517	0.84[CEU][hapmap];0.94[MEX][hapmap]
rs696518	0.93[JPT][hapmap]
rs696520	1.00[JPT][hapmap]
rs698270	0.89[CHB][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs72493178	0.85[ASN][1000 genomes]
rs73222262	0.84[ASN][1000 genomes]
rs7372313	0.86[JPT][hapmap]
rs7628146	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7653249	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs834304	0.85[JPT][hapmap]
rs864437	0.87[JPT][hapmap]
rs866758	0.87[JPT][hapmap]
rs895894	0.86[JPT][hapmap]
rs9832056	0.89[CHB][hapmap]
rs9832813	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs9840812	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs9845457	0.86[JPT][hapmap]
rs9848883	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[ASN][1000 genomes]
rs9851986	0.89[CHB][hapmap]
rs9854084	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9856769	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[ASN][1000 genomes]
rs9869720	0.89[CHB][hapmap]

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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1279840	PCCB	cis	lymphoblastoid	seeQTL
rs1279840	MSL2	cis	cerebellum	SCAN
rs1279840	NCK1	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:135976200-136012400	Weak transcription	NHLF	lung
3	chr3:135976200-136016400	Weak transcription	Colonic Mucosa	Colon
4	chr3:135976200-136021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:135981200-136052000	Weak transcription	NH-A	brain
6	chr3:135981600-136020400	Weak transcription	HUVEC	blood vessel
7	chr3:135996800-136016000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:135997000-136010600	Weak transcription	Gastric	stomach
9	chr3:135997000-136012000	Weak transcription	Spleen	Spleen
10	chr3:135997400-136015200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:135998000-136040200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:135999800-136013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:135999800-136013000	Weak transcription	Small Intestine	intestine
14	chr3:135999800-136016200	Weak transcription	Esophagus	oesophagus
15	chr3:135999800-136016800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:135999800-136019000	Weak transcription	NHEK	skin
17	chr3:135999800-136038200	Weak transcription	Fetal Brain Male	brain
18	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
19	chr3:136000000-136016600	Weak transcription	Thymus	Thymus
20	chr3:136000000-136024600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:136000200-136008200	Strong transcription	Dnd41	blood
22	chr3:136000200-136012200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:136000200-136038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:136001200-136006800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:136001200-136008200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:136001200-136011400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:136001200-136016400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:136001200-136019200	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:136001400-136008200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:136001600-136006800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:136001600-136007600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:136001800-136006600	Strong transcription	Primary hematopoietic stem cells	blood
33	chr3:136001800-136007200	Strong transcription	Primary T cells from cord blood	blood
34	chr3:136001800-136007600	Strong transcription	Liver	Liver
35	chr3:136002000-136007000	Strong transcription	Duodenum Mucosa	Duodenum
36	chr3:136002000-136007000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr3:136002000-136007600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:136002000-136007600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:136002000-136007800	Strong transcription	Fetal Stomach	stomach
40	chr3:136002000-136008000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:136002000-136017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:136002200-136006600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr3:136002200-136006600	Strong transcription	Brain Substantia Nigra	brain
44	chr3:136002200-136006800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:136002200-136007000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:136002200-136007000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:136002200-136008200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:136002200-136012400	Weak transcription	Brain Angular Gyrus	brain
49	chr3:136002200-136014800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:136002200-136015600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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