Variant report

Variant	rs1432838
Chromosome Location	chr5:146762381-146762382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:146762276-146762668	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:146762369-146762637	MCF-7	breast:	n/a	n/a
3	RFX5	chr5:146762335-146762549	Hela-S3	cervix:	n/a	n/a
4	YY1	chr5:146762293-146762524	HCT-116	colon:	n/a	n/a
5	POLR2A	chr5:146762350-146762656	Hela-S3	cervix:	n/a	n/a
6	SP1	chr5:146762182-146762587	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr5:146762333-146762617	Hela-S3	cervix:	n/a	n/a
8	YY1	chr5:146762245-146762951	H1-hESC	embryonic stem cell:	n/a	chr5:146762864-146762876
9	GTF2F1	chr5:146762375-146762532	Hela-S3	cervix:	n/a	n/a
10	YY1	chr5:146762313-146762583	H1-hESC	embryonic stem cell:	n/a	n/a
11	ZNF143	chr5:146762265-146762584	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr5:146762164-146762778	U87	brain:	n/a	n/a
13	TBP	chr5:146762240-146763062	Hela-S3	cervix:	n/a	n/a
14	MAX	chr5:146762288-146762762	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr5:146762277-146762677	ProgFib	skin:	n/a	n/a
16	ZNF143	chr5:146762277-146762653	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr5:146762255-146762589	HCT-116	colon:	n/a	n/a
18	TAF1	chr5:146762264-146762595	PFSK-1	brain:	n/a	n/a
19	MAX	chr5:146762330-146762745	Hela-S3	cervix:	n/a	n/a
20	CHD2	chr5:146762306-146762631	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr5:146762236-146762658	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
STK32A	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10042298	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10515581	0.87[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs10515582	0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs10515583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11167988	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11167989	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12513884	0.90[ASN][1000 genomes]
rs12514302	1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs12518250	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12520080	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12520257	0.81[ASN][1000 genomes]
rs12520436	0.85[JPT][hapmap]
rs12651731	0.93[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1432839	0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1432854	0.80[CHB][hapmap]
rs1432855	0.80[CHB][hapmap]
rs1432856	0.80[CHB][hapmap]
rs1432857	0.85[CHB][hapmap]
rs1544816	0.85[ASN][1000 genomes]
rs17106470	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs17106482	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs17106492	0.87[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs17106560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17106572	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17106575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17106590	0.99[ASN][1000 genomes]
rs17106592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17106597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17106606	0.95[ASN][1000 genomes]
rs17106607	0.86[CHD][hapmap];0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17106679	0.80[CHB][hapmap]
rs17106682	0.80[CHB][hapmap]
rs17106683	0.80[CHB][hapmap]
rs17106686	0.80[CHB][hapmap]
rs17106688	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs17106689	0.80[CHB][hapmap]
rs17106690	0.80[CHB][hapmap]
rs2288800	0.80[CHB][hapmap]
rs2288805	0.87[CHB][hapmap];0.80[CHD][hapmap];0.93[JPT][hapmap]
rs2288809	0.87[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap]
rs2895681	0.90[ASN][1000 genomes]
rs3213857	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs3749721	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3792837	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs3792839	0.80[CHB][hapmap]
rs3792840	0.85[JPT][hapmap]
rs3792844	0.80[CHB][hapmap]
rs3792846	0.80[CHB][hapmap]
rs3805533	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3805534	0.93[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs3805535	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs3805540	0.80[CHB][hapmap]
rs3816012	0.80[CHB][hapmap]
rs4642416	0.90[ASN][1000 genomes]
rs61405762	0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6891468	0.80[CHB][hapmap]
rs73262265	0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7714240	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs972302	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146747800-146762400	Weak transcription	Fetal Kidney	kidney
2	chr5:146750000-146766200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:146755600-146762400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:146758200-146762400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:146760000-146762400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:146761800-146765800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:146762000-146762400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr5:146762000-146762800	Active TSS	Aorta	Aorta
9	chr5:146762200-146762400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:146762200-146762400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr5:146762200-146762400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr5:146762200-146762400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr5:146762200-146762400	Enhancers	Adipose Nuclei	Adipose
14	chr5:146762200-146762400	Enhancers	Placenta	Placenta
15	chr5:146762200-146762400	Flanking Active TSS	Rectal Smooth Muscle	rectum
16	chr5:146762200-146762600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:146762200-146762800	Enhancers	H9 Cell Line	embryonic stem cell
18	chr5:146762200-146762800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:146762200-146762800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:146762200-146762800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr5:146762200-146762800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:146762200-146762800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:146762200-146762800	Active TSS	Brain Cingulate Gyrus	brain
24	chr5:146762200-146763000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr5:146762200-146763000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr5:146762200-146763000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:146762200-146763000	Active TSS	Brain Anterior Caudate	brain
28	chr5:146762200-146763000	Active TSS	Colon Smooth Muscle	Colon
29	chr5:146762200-146763000	Active TSS	Stomach Smooth Muscle	stomach
30	chr5:146762200-146763000	Active TSS	Hela-S3	cervix
31	chr5:146762200-146763000	Active TSS	NHDF-Ad	bronchial
32	chr5:146762200-146763200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr5:146762200-146763200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:146762200-146763200	Active TSS	Brain Angular Gyrus	brain
35	chr5:146762200-146763200	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr5:146762200-146764000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:146762200-146764800	Active TSS	Ovary	ovary

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