Variant report

Variant	rs4678428
Chromosome Location	chr3:135988412-135988413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

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]
rs1145106	0.90[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs1153871	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1153877	1.00[JPT][hapmap]
rs1154988	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs11715257	0.93[JPT][hapmap]
rs11717954	0.87[JPT][hapmap]
rs12330635	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12492510	0.87[JPT][hapmap]
rs1278493	0.86[JPT][hapmap]
rs1278719	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1279086	1.00[JPT][hapmap]
rs1279425	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1279831	0.86[JPT][hapmap]
rs1279840	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]
rs1291921	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1618069	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2655008	0.93[JPT][hapmap]
rs3755636	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3772390	0.88[CHB][hapmap]
rs3821445	0.84[CEU][hapmap]
rs3957816	0.86[JPT][hapmap]
rs483465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs518972	1.00[JPT][hapmap]
rs521746	0.87[JPT][hapmap]
rs523118	0.82[EUR][1000 genomes]
rs534944	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs548288	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs553018	0.93[JPT][hapmap]
rs556788	1.00[JPT][hapmap]
rs571513	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs576771	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs589092	1.00[JPT][hapmap]
rs595532	0.93[JPT][hapmap]
rs606725	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs610860	0.84[CEU][hapmap]
rs619605	0.93[JPT][hapmap]
rs632016	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6439638	0.85[YRI][hapmap]
rs645040	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs650326	1.00[JPT][hapmap]
rs650505	0.99[ASN][1000 genomes]
rs654237	0.93[JPT][hapmap]
rs655836	0.93[JPT][hapmap]
rs661739	0.86[JPT][hapmap]
rs665200	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667920	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6770476	0.80[ASN][1000 genomes]
rs6791611	0.87[JPT][hapmap]
rs684773	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs687339	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs695983	0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs696081	1.00[JPT][hapmap]
rs696516	0.85[CEU][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs696517	0.84[CEU][hapmap]
rs696518	0.93[JPT][hapmap]
rs696520	1.00[JPT][hapmap]
rs698270	0.89[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap]
rs72493178	0.88[ASN][1000 genomes]
rs73222262	0.87[ASN][1000 genomes]
rs7372313	0.86[JPT][hapmap]
rs7628146	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653249	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs834304	0.85[JPT][hapmap]
rs864437	0.87[JPT][hapmap]
rs866758	0.87[JPT][hapmap]
rs895894	0.86[JPT][hapmap]
rs9826146	0.86[YRI][hapmap]
rs9831321	0.89[YRI][hapmap]
rs9832056	0.89[CHB][hapmap]
rs9832813	0.89[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs9840812	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs9843801	0.86[YRI][hapmap]
rs9845457	0.86[JPT][hapmap]
rs9848883	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[ASN][1000 genomes]
rs9851986	0.89[CHB][hapmap];0.83[CHD][hapmap]
rs9853387	0.82[YRI][hapmap]
rs9856769	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[ASN][1000 genomes]
rs9860801	0.82[YRI][hapmap]
rs9868120	0.89[YRI][hapmap]
rs9869720	0.89[CHB][hapmap];0.82[CHD][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4678428	PCCB	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970200-135996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:135970400-135995400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:135970600-135998800	Weak transcription	Fetal Brain Male	brain
4	chr3:135970600-135999200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:135970600-135999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:135970800-135995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:135970800-135998000	Weak transcription	Hela-S3	cervix
9	chr3:135974000-135989400	Strong transcription	Dnd41	blood
10	chr3:135974200-135989600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:135974200-135989600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:135974400-135989600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:135974800-135997800	Weak transcription	Stomach Mucosa	stomach
14	chr3:135976200-135996000	Weak transcription	Pancreas	Pancrea
15	chr3:135976200-135999400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:135976200-136012400	Weak transcription	NHLF	lung
17	chr3:135976200-136016400	Weak transcription	Colonic Mucosa	Colon
18	chr3:135976200-136021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:135976400-135989000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:135977400-135995600	Weak transcription	Fetal Lung	lung
21	chr3:135977400-135996000	Weak transcription	K562	blood
22	chr3:135977600-135995400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:135977800-135993600	Weak transcription	Fetal Kidney	kidney
24	chr3:135980800-135995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:135980800-135995600	Weak transcription	Right Ventricle	heart
26	chr3:135980800-135997600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:135980800-135999200	Weak transcription	Small Intestine	intestine
28	chr3:135981000-135995200	Weak transcription	Brain Germinal Matrix	brain
29	chr3:135981000-135995400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:135981000-135995400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:135981000-135998600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:135981200-135999200	Weak transcription	NHDF-Ad	bronchial
33	chr3:135981200-136052000	Weak transcription	NH-A	brain
34	chr3:135981600-135995000	Weak transcription	Psoas Muscle	Psoas
35	chr3:135981600-135995200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:135981600-135997200	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:135981600-135998000	Weak transcription	Fetal Heart	heart
38	chr3:135981600-135998800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:135981600-136020400	Weak transcription	HUVEC	blood vessel
40	chr3:135981800-135995000	Weak transcription	Brain Substantia Nigra	brain
41	chr3:135981800-135995600	Weak transcription	Gastric	stomach
42	chr3:135981800-135999600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:135982400-135995200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:135982600-135991400	Weak transcription	NHEK	skin
45	chr3:135982600-135997800	Weak transcription	HSMMtube	muscle
46	chr3:135982600-135999000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:135982600-136004000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:135982800-135995400	Weak transcription	Left Ventricle	heart
49	chr3:135982800-135995600	Weak transcription	Lung	lung
50	chr3:135982800-135995800	Weak transcription	Primary T cells fromperipheralblood	blood

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