Variant report

Variant	rs549914
Chromosome Location	chr15:55669784-55669785
allele	G/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	chr15:55669195-55670246	K562	blood:	n/a	n/a
2	STAT3	chr15:55669752-55670203	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55659460..55661361-chr15:55668355..55670079,2	K562	blood:

Variant related genes	Relation type
MIR628	TF binding region
CCPG1	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11071184	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11071185	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs11071186	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11637024	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148682	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs12324434	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs12900382	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12908712	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12910693	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12913017	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12913182	0.82[AMR][1000 genomes]
rs1624851	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414415	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2439045	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439047	0.91[AMR][1000 genomes]
rs2447712	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4144134	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs472579	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774210	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774211	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774768	0.80[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs493968	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs501231	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	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600753	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60229152	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs606446	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs646322	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493789	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6493791	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs685935	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[YRI][hapmap]
rs691447	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs692636	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs692646	0.85[ASW][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs692690	0.85[ASW][hapmap];1.00[YRI][hapmap]
rs7168202	0.88[ASN][1000 genomes]
rs7169179	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7169948	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7170993	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174641	0.80[MEX][hapmap]
rs7174810	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8042996	0.92[ASW][hapmap];0.89[GIH][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs9920450	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	nsv1041635	chr15:55658171-55943942	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs549914	PIGB	cis	lymphoblastoid	seeQTL
rs549914	TTC13	trans	brain	seeQTL
rs549914	TNFAIP8L3	cis	parietal	SCAN

Chromatin state (count:106 , 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	chr15:55612000-55671000	Weak transcription	Right Ventricle	heart
3	chr15:55612000-55671000	Weak transcription	Small Intestine	intestine
4	chr15:55612600-55675600	Weak transcription	Aorta	Aorta
5	chr15:55612800-55677600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:55630000-55695000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:55630400-55675600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:55630800-55683600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:55631200-55674000	Weak transcription	Placenta	Placenta
10	chr15:55635800-55675200	Weak transcription	Fetal Brain Male	brain
11	chr15:55636600-55678200	Weak transcription	Fetal Thymus	thymus
12	chr15:55637000-55671400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:55637000-55699600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:55637400-55680200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:55641000-55671600	Weak transcription	Thymus	Thymus
16	chr15:55645000-55680800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:55645600-55681400	Weak transcription	Stomach Mucosa	stomach
18	chr15:55647800-55695400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:55648800-55675800	Weak transcription	Dnd41	blood
20	chr15:55649200-55681000	Weak transcription	HSMM	muscle
21	chr15:55649800-55695800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:55650800-55680800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:55651000-55675200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:55652800-55675800	Weak transcription	NHDF-Ad	bronchial
25	chr15:55653000-55675200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:55659600-55672200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:55659600-55682000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr15:55660200-55672200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:55661200-55671000	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:55661200-55672000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr15:55661200-55680800	Weak transcription	NHLF	lung
32	chr15:55661400-55671000	Weak transcription	Gastric	stomach
33	chr15:55661400-55671400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr15:55662200-55681600	Weak transcription	Esophagus	oesophagus
35	chr15:55662400-55669800	Strong transcription	Brain Anterior Caudate	brain
36	chr15:55662600-55672200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr15:55662800-55674000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr15:55663400-55672000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:55664000-55675400	Weak transcription	Fetal Lung	lung
40	chr15:55664200-55671000	Weak transcription	Brain Angular Gyrus	brain
41	chr15:55664200-55675000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:55664200-55681200	Weak transcription	NH-A	brain
43	chr15:55665200-55672200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:55665400-55670600	Strong transcription	Primary B cells from cord blood	blood
45	chr15:55665400-55671000	Weak transcription	Fetal Intestine Small	intestine
46	chr15:55665600-55672200	Strong transcription	Liver	Liver
47	chr15:55665800-55672200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr15:55665800-55675200	Weak transcription	Fetal Kidney	kidney
49	chr15:55665800-55676800	Weak transcription	HepG2	liver
50	chr15:55665800-55680800	Weak transcription	A549	lung

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