Variant report

Variant	rs748630
Chromosome Location	chr4:128901402-128901403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:128894875..128896816-chr4:128900805..128902998,2	K562	blood:

Extended variants
information (count: 120 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10000960	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs10001048	0.87[CEU][hapmap]
rs1001503	0.87[CEU][hapmap]
rs10019554	0.87[CEU][hapmap]
rs10019840	0.87[CEU][hapmap]
rs10026899	0.96[CEU][hapmap]
rs10493147	0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs10518529	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs1064205	0.95[CEU][hapmap];0.82[GIH][hapmap]
rs10857126	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs10857128	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs10857129	0.96[CEU][hapmap];0.83[GIH][hapmap];0.94[MKK][hapmap]
rs11098940	0.87[CEU][hapmap]
rs11098947	0.87[CEU][hapmap]
rs11098950	0.91[CEU][hapmap]
rs11723915	0.87[CEU][hapmap]
rs11725843	0.87[EUR][1000 genomes]
rs11727049	0.87[CEU][hapmap]
rs11727305	0.95[CEU][hapmap]
rs11735635	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11735810	0.96[CEU][hapmap];0.82[GIH][hapmap]
rs12503257	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12504266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504825	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12505717	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs12506549	0.96[CEU][hapmap];0.82[GIH][hapmap]
rs12509092	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs12510785	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641548	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs12645577	0.96[CEU][hapmap];0.80[GIH][hapmap]
rs12645636	0.92[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs13102049	0.96[CEU][hapmap];0.85[GIH][hapmap]
rs13122568	0.83[GIH][hapmap]
rs13127610	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13135183	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13135526	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138581	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs13139182	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs1380154	0.91[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs1380156	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap]
rs1459050	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap]
rs1545711	0.83[CEU][hapmap]
rs16997980	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs17012739	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1870422	0.87[CEU][hapmap]
rs1870686	0.95[CEU][hapmap]
rs1870687	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs1975878	0.91[CEU][hapmap];0.80[GIH][hapmap]
rs1975879	0.91[CEU][hapmap]
rs1993722	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs2061570	0.96[CEU][hapmap];0.85[GIH][hapmap]
rs2061571	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs2061572	0.82[CEU][hapmap]
rs2087446	0.88[EUR][1000 genomes]
rs2126112	0.87[CEU][hapmap]
rs2305957	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2306054	0.95[CEU][hapmap];0.83[GIH][hapmap]
rs2306055	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs2391231	0.96[CEU][hapmap];0.82[GIH][hapmap];0.94[MKK][hapmap]
rs34625382	0.84[EUR][1000 genomes]
rs3733320	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs3811740	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3811741	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[MKK][hapmap];0.81[ASN][1000 genomes]
rs4383632	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs4385082	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs4484314	0.87[CEU][hapmap];0.83[GIH][hapmap]
rs4493552	0.87[CEU][hapmap]
rs4833393	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4833395	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs4834223	0.92[CEU][hapmap]
rs4834224	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs4834225	0.92[CEU][hapmap];0.88[TSI][hapmap]
rs4834226	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs4834229	0.96[CEU][hapmap]
rs4834231	0.87[CEU][hapmap]
rs4834234	0.96[CEU][hapmap]
rs6534647	0.87[EUR][1000 genomes]
rs6534648	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6534655	0.88[EUR][1000 genomes]
rs6534656	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534658	0.86[EUR][1000 genomes]
rs6534659	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs6534668	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs6811718	0.87[CEU][hapmap]
rs6815890	0.96[CEU][hapmap]
rs6818467	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs6829891	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs6839292	0.87[CEU][hapmap]
rs6839370	0.96[CEU][hapmap]
rs6846535	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6849546	0.95[CEU][hapmap];0.83[GIH][hapmap]
rs6851796	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs7441217	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7661888	0.96[CEU][hapmap];0.85[GIH][hapmap]
rs7671131	0.83[CEU][hapmap]
rs7671590	0.87[CEU][hapmap]
rs7684368	0.87[CEU][hapmap]
rs7686130	0.87[CEU][hapmap]
rs7692740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9968459	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap]
rs9993435	0.96[CEU][hapmap];0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv879922	chr4:128554404-128901402	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1801492	chr4:128566686-128934513	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	esv3431515	chr4:128657260-128932577	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv532740	chr4:128710011-129035335	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	esv3416036	chr4:128782694-129133956	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1033701	chr4:128803159-129095018	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv1019193	chr4:128810527-128949320	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv1841203	chr4:128817558-129043809	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
14	nsv1029890	chr4:128828468-129041302	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
15	esv1817670	chr4:128850073-129012181	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
16	esv1821180	chr4:128850073-129012181	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
17	nsv1018952	chr4:128850790-129082821	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
18	nsv595388	chr4:128853913-129084831	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs748630	LARP1B	cis	parietal	SCAN
rs748630	PLK4	cis	cerebellum	SCAN
rs748630	C4orf29	cis	parietal	SCAN
rs748630	LARP2	cis	multi-tissue	Pritchard
rs748630	HSPA4L	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128887400-128905600	Weak transcription	Placenta	Placenta
2	chr4:128887400-128909400	Weak transcription	Ovary	ovary
3	chr4:128887400-128912200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:128887600-128904600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:128887600-128905600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:128887600-128907200	Weak transcription	HSMMtube	muscle
7	chr4:128887600-128910000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:128887600-128920800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:128887600-128933600	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:128887600-128933800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:128887600-128941400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:128887600-128981200	Weak transcription	Psoas Muscle	Psoas
13	chr4:128887800-128905400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:128887800-128912800	Weak transcription	Fetal Brain Male	brain
15	chr4:128887800-128917200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:128887800-128921000	Weak transcription	Fetal Lung	lung
17	chr4:128887800-128930400	Weak transcription	Osteobl	bone
18	chr4:128887800-128933800	Weak transcription	Gastric	stomach
19	chr4:128887800-128940200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:128887800-128941200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:128887800-128951200	Weak transcription	HUVEC	blood vessel
22	chr4:128888400-128905400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:128888400-128913400	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:128888400-128921400	Weak transcription	Brain Anterior Caudate	brain
25	chr4:128888400-128941200	Weak transcription	NHDF-Ad	bronchial
26	chr4:128888400-128956000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr4:128888600-128933200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:128888800-128905400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:128888800-128905600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:128888800-128914200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:128890200-128933600	Weak transcription	Aorta	Aorta
32	chr4:128890200-128939200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:128890200-128950600	Weak transcription	HepG2	liver
34	chr4:128890400-128958600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr4:128890600-128905400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:128892400-128908200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:128892400-128912000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:128893600-128905400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:128893600-128948200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr4:128893600-128954200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr4:128893600-128955800	Weak transcription	Right Ventricle	heart
42	chr4:128894200-128916200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr4:128894600-128919400	Weak transcription	Fetal Kidney	kidney
44	chr4:128894800-128917000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:128895200-128905200	Weak transcription	Liver	Liver
46	chr4:128895600-128905400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr4:128895600-128905400	Weak transcription	K562	blood
48	chr4:128895600-128905600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr4:128895800-128903800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr4:128895800-128904600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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