Variant report

Variant	rs12503257
Chromosome Location	chr4:128832078-128832079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10024450	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10493147	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1064205	1.00[CEU][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap]
rs10857126	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10857128	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs11098936	0.84[CEU][hapmap]
rs11098937	0.81[CHD][hapmap]
rs11098940	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs11098947	0.92[CEU][hapmap]
rs11098950	0.95[CEU][hapmap]
rs11725843	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11735635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12504266	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12504825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12506549	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs12510785	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12511932	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs12641548	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs12645068	0.87[EUR][1000 genomes]
rs12645636	0.88[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap]
rs13102049	1.00[CEU][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs13122568	0.81[CHD][hapmap]
rs13127610	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs1380154	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1380156	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1459048	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.84[ASN][1000 genomes]
rs1459050	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1585312	0.84[CEU][hapmap]
rs16997980	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs17012739	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1870422	0.92[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs1903104	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs1975878	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs1975879	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs1993722	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs2085655	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2087446	0.81[EUR][1000 genomes]
rs2126112	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2305957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305958	0.84[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap]
rs2306054	1.00[CEU][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs3214038	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34625382	0.81[EUR][1000 genomes]
rs3775982	0.82[CEU][hapmap]
rs3811740	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3811741	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3816588	0.86[CEU][hapmap]
rs4435753	0.84[CEU][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap]
rs4833391	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4833393	0.83[EUR][1000 genomes]
rs4833395	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs4834217	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs4834223	0.88[CEU][hapmap]
rs4834224	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap]
rs4834225	0.88[CEU][hapmap];0.88[TSI][hapmap]
rs4834226	1.00[CEU][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs4834229	1.00[CEU][hapmap]
rs4834231	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs55798529	0.83[EUR][1000 genomes]
rs62335590	0.85[EUR][1000 genomes]
rs6534638	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6534647	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6534648	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6534656	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6534659	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs6821748	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6839292	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs6839370	1.00[CEU][hapmap]
rs6846535	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7376138	0.82[EUR][1000 genomes]
rs7441217	0.81[ASN][1000 genomes]
rs748630	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7654638	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs7661888	1.00[CEU][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs7671131	0.87[CEU][hapmap]
rs7671590	0.92[CEU][hapmap]
rs7684368	0.92[CEU][hapmap]
rs7686130	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs7692740	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs769293	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs959822	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9968459	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9995738	0.84[CEU][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	esv1793579	chr4:128577439-128871309	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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
15	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
16	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12503257	C4orf29	cis	parietal	SCAN
rs12503257	PLK4	cis	cerebellum	SCAN
rs12503257	LARP1B	cis	parietal	SCAN
rs12503257	HSPA4L	cis	cerebellum	SCAN
rs12503257	HSPA4L	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128803400-128841800	Weak transcription	Brain Germinal Matrix	brain
2	chr4:128814000-128838200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:128815000-128839200	Weak transcription	NHDF-Ad	bronchial
4	chr4:128815400-128839400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr4:128817400-128839800	Weak transcription	HSMM	muscle
6	chr4:128817400-128841600	Weak transcription	Thymus	Thymus
7	chr4:128817400-128849400	Weak transcription	Osteobl	bone
8	chr4:128818400-128838400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr4:128818800-128837800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr4:128818800-128863000	Weak transcription	A549	lung
11	chr4:128820000-128839200	Weak transcription	HMEC	breast
12	chr4:128820200-128833200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:128820400-128835000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:128821000-128838800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:128821000-128841600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:128821200-128837800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:128821200-128838000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:128821200-128838000	Weak transcription	Dnd41	blood
19	chr4:128821200-128838400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:128821200-128839000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:128826600-128841600	Weak transcription	K562	blood
22	chr4:128830600-128838200	Weak transcription	Placenta	Placenta
23	chr4:128831000-128841600	Weak transcription	HepG2	liver
24	chr4:128831200-128884600	Weak transcription	Spleen	Spleen
25	chr4:128832000-128841600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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