Variant report

Variant	rs501231
Chromosome Location	chr15:55653031-55653032
allele	C/T
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	chr15:55644269-55653358	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55622982..55625062-chr15:55652852..55654704,2	MCF-7	breast:

Variant related genes	Relation type
CCPG1	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11071184	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11071185	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11071186	0.92[ASN][1000 genomes]
rs11637024	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12148682	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12324434	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs12900382	0.90[ASN][1000 genomes]
rs12908712	0.93[ASN][1000 genomes]
rs12910693	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913017	0.84[ASN][1000 genomes]
rs1624851	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414415	0.89[ASN][1000 genomes]
rs2439045	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2439047	0.81[AMR][1000 genomes]
rs2447712	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4144134	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs472579	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774210	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774211	0.94[ASN][1000 genomes]
rs4774768	0.92[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs493968	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs549914	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs593556	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs600753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs60229152	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs606446	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs646322	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493789	0.85[ASN][1000 genomes]
rs6493791	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs685935	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs691447	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs692636	0.84[ASN][1000 genomes]
rs7168202	0.87[ASN][1000 genomes]
rs7169179	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7169948	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7170993	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174641	0.85[JPT][hapmap]
rs7174810	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8042996	0.93[GIH][hapmap];0.85[JPT][hapmap]
rs9920450	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv904243	chr15:55627528-55734158	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv520799	chr15:55645661-55760522	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs501231	PIGB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
2	chr15:55612000-55665000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr15:55612000-55671000	Weak transcription	Right Ventricle	heart
4	chr15:55612000-55671000	Weak transcription	Small Intestine	intestine
5	chr15:55612600-55663600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:55612600-55675600	Weak transcription	Aorta	Aorta
7	chr15:55612800-55677600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:55620400-55658000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:55623800-55660200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:55630000-55695000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:55630400-55654600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:55630400-55675600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:55630600-55655800	Weak transcription	Brain Angular Gyrus	brain
14	chr15:55630600-55660200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:55630600-55663200	Weak transcription	Fetal Lung	lung
16	chr15:55630600-55667800	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:55630600-55668400	Weak transcription	Brain Substantia Nigra	brain
18	chr15:55630800-55683600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:55631000-55667800	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:55631200-55663200	Weak transcription	Pancreas	Pancrea
21	chr15:55631200-55674000	Weak transcription	Placenta	Placenta
22	chr15:55633600-55667200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:55635800-55675200	Weak transcription	Fetal Brain Male	brain
24	chr15:55636600-55657000	Weak transcription	Fetal Brain Female	brain
25	chr15:55636600-55678200	Weak transcription	Fetal Thymus	thymus
26	chr15:55636800-55666200	Weak transcription	Brain Germinal Matrix	brain
27	chr15:55637000-55660400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:55637000-55663000	Weak transcription	K562	blood
29	chr15:55637000-55663400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:55637000-55671400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:55637000-55699600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:55637400-55680200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:55638000-55658200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr15:55641000-55654800	Weak transcription	HSMMtube	muscle
35	chr15:55641000-55655200	Weak transcription	Lung	lung
36	chr15:55641000-55667800	Weak transcription	Spleen	Spleen
37	chr15:55641000-55668000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:55641000-55671600	Weak transcription	Thymus	Thymus
39	chr15:55641200-55658200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:55641600-55660200	Weak transcription	Gastric	stomach
41	chr15:55643000-55664000	Weak transcription	GM12878-XiMat	blood
42	chr15:55643200-55656400	Weak transcription	Hela-S3	cervix
43	chr15:55644800-55654600	Weak transcription	Brain Anterior Caudate	brain
44	chr15:55645000-55653400	Weak transcription	Fetal Stomach	stomach
45	chr15:55645000-55665000	Weak transcription	Fetal Intestine Small	intestine
46	chr15:55645000-55667800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:55645000-55680800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:55645200-55657400	Strong transcription	Liver	Liver
49	chr15:55645600-55681400	Weak transcription	Stomach Mucosa	stomach
50	chr15:55646400-55656200	Strong transcription	Skeletal Muscle Female	skeletal muscle

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