Variant report

Variant	rs6493430
Chromosome Location	chr15:50642916-50642917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:50641221-50643664	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:50642011-50646578	K562	blood:	n/a	n/a
3	POLR2A	chr15:50642794-50643429	A549	lung:	n/a	n/a
4	POLR2A	chr15:50642679-50643644	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50642251..50643809-chr15:50770828..50773019,2	MCF-7	breast:
2	chr15:50474061..50475974-chr15:50641012..50643370,2	MCF-7	breast:
3	chr15:50642734..50644245-chr15:50716528..50719210,2	K562	blood:
4	chr15:50619418..50621400-chr15:50642580..50644412,2	MCF-7	breast:
5	chr15:50641443..50644268-chr15:50716209..50717916,2	MCF-7	breast:
6	chr15:50487139..50490001-chr15:50641333..50643043,2	K562	blood:
7	chr15:50479666..50482276-chr15:50642111..50643879,2	MCF-7	breast:
8	chr15:50642199..50645387-chr15:50753555..50756169,3	MCF-7	breast:
9	chr15:50625762..50628715-chr15:50641413..50643751,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HDC-2	chr15:50641135-50647076	NONHSAT042404

No data

Variant related genes	Relation type
ENSG00000271819	TF binding region
GABPB1-AS1	TF binding region
ENSG00000138592	Chromatin interaction
ENSG00000104043	Chromatin interaction
ENSG00000252376	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000140284	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10152534	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10220734	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10220755	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11070766	0.83[EUR][1000 genomes]
rs11070768	0.84[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs11629603	0.84[EUR][1000 genomes]
rs11630045	0.82[EUR][1000 genomes]
rs11631985	0.83[EUR][1000 genomes]
rs11632703	0.84[CEU][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs11633903	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11636564	0.84[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs11637901	0.83[EUR][1000 genomes]
rs11638319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11638432	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs11638564	0.82[EUR][1000 genomes]
rs11639406	0.84[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs11852487	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs11853236	0.84[EUR][1000 genomes]
rs11855823	0.84[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs12594956	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12901373	0.95[ASN][1000 genomes]
rs12902318	0.84[CEU][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs12910586	0.81[EUR][1000 genomes]
rs12912969	0.83[EUR][1000 genomes]
rs12913144	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1365504	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1645	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs16963604	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs16963612	0.84[EUR][1000 genomes]
rs17508371	0.80[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs1797311	0.88[CEU][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1972699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033115	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs2081628	0.84[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs2114447	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs28372114	0.83[EUR][1000 genomes]
rs28609286	0.84[EUR][1000 genomes]
rs28669213	0.83[EUR][1000 genomes]
rs28688566	0.83[EUR][1000 genomes]
rs28715646	0.85[EUR][1000 genomes]
rs28716586	0.83[EUR][1000 genomes]
rs28886692	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34197276	0.84[EUR][1000 genomes]
rs34590486	0.83[EUR][1000 genomes]
rs35000991	0.81[EUR][1000 genomes]
rs35024305	0.84[EUR][1000 genomes]
rs35168369	0.84[EUR][1000 genomes]
rs35777196	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3784297	0.90[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3985829	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4775874	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4775875	0.83[EUR][1000 genomes]
rs4775876	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs4775877	0.83[EUR][1000 genomes]
rs489345	0.94[ASN][1000 genomes]
rs526045	0.84[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs535648	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62022573	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493425	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493427	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493429	0.84[EUR][1000 genomes]
rs7163457	0.84[CEU][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs7168233	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173127	0.80[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs7176792	0.82[EUR][1000 genomes]
rs7179819	0.83[AFR][1000 genomes]
rs8025367	0.82[EUR][1000 genomes]
rs8026571	0.83[EUR][1000 genomes]
rs8026785	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8027367	0.82[EUR][1000 genomes]
rs8030036	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8031431	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8034615	0.83[EUR][1000 genomes]
rs8036354	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs8039829	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8041259	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8042451	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8042845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8043257	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs6493430	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs6493430	CTD-3110H11.1	cis	lung	GTEx
rs6493430	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs6493430	GABPB1-AS1	cis	Artery Tibial	GTEx
rs6493430	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs6493430	GABPB2	cis	uninvolved skin	skin_eQTL
rs6493430	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs6493430	CTD-3110H11.1	cis	Thyroid	GTEx
rs6493430	GABPB2	cis	normal skin	skin_eQTL
rs6493430	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs6493430	GABPB1-AS1	cis	lung	GTEx
rs6493430	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs6493430	GABPB2	cis	lesional skin	skin_eQTL
rs6493430	GABPB1-AS1	cis	Artery Aorta	GTEx
rs6493430	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs6493430	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs6493430	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs6493430	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs6493430	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs6493430	CTD-3110H11.1	cis	Artery Tibial	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50600800-50643000	Weak transcription	Fetal Thymus	thymus
2	chr15:50600800-50643400	Weak transcription	Fetal Muscle Leg	muscle
3	chr15:50600800-50644200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:50600800-50644600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:50615200-50644000	Weak transcription	HSMMtube	muscle
6	chr15:50618400-50646000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:50621200-50646000	Weak transcription	Gastric	stomach
8	chr15:50623400-50643000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:50623800-50644200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:50623800-50645600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:50624000-50644000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:50624000-50644000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:50624000-50644000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:50627600-50643000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:50627800-50643600	Weak transcription	Lung	lung
16	chr15:50628400-50643600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:50630000-50643600	Weak transcription	Placenta	Placenta
18	chr15:50631000-50643400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:50631400-50643400	Weak transcription	Fetal Stomach	stomach
20	chr15:50631400-50643800	Weak transcription	Fetal Intestine Small	intestine
21	chr15:50633800-50645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:50635800-50643600	Weak transcription	Psoas Muscle	Psoas
23	chr15:50638800-50644000	Weak transcription	HMEC	breast
24	chr15:50638800-50644600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:50639200-50644000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:50639400-50643400	Weak transcription	Left Ventricle	heart
27	chr15:50639800-50643000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr15:50640600-50644000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr15:50641000-50643600	Weak transcription	Spleen	Spleen
30	chr15:50641000-50644800	Weak transcription	Ovary	ovary
31	chr15:50641000-50645600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:50641200-50643000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr15:50641200-50643000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:50641200-50643400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:50641200-50644600	Enhancers	HepG2	liver
36	chr15:50641400-50643400	Enhancers	A549	lung
37	chr15:50641400-50643600	Enhancers	Brain Anterior Caudate	brain
38	chr15:50641400-50644000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr15:50641400-50644000	Enhancers	NHEK	skin
40	chr15:50641400-50644200	Enhancers	Colon Smooth Muscle	Colon
41	chr15:50641400-50644600	Enhancers	Brain Hippocampus Middle	brain
42	chr15:50641600-50643000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr15:50641600-50643000	Enhancers	Fetal Kidney	kidney
44	chr15:50641600-50643200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:50641600-50643200	Enhancers	HUVEC	blood vessel
46	chr15:50641600-50643400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:50641600-50643400	Enhancers	NHLF	lung
48	chr15:50641600-50643600	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr15:50641600-50644000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:50641600-50644000	Enhancers	Liver	Liver

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