Variant report

Variant	rs9920450
Chromosome Location	chr15:55693204-55693205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55609981..55613646-chr15:55692667..55696745,4	K562	blood:
2	chr15:55686108..55691081-chr15:55692026..55698243,11	K562	blood:

Variant related genes	Relation type
ENSG00000260916	Chromatin interaction
ENSG00000225973	Chromatin interaction
ENSG00000069943	Chromatin interaction
ENSG00000069974	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11071184	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11071185	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[ASN][1000 genomes]
rs11071186	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11637024	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12324434	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12440680	0.91[AFR][1000 genomes]
rs12900382	0.94[ASN][1000 genomes]
rs12903949	0.93[AFR][1000 genomes]
rs12908712	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910693	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913017	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12913182	0.80[ASN][1000 genomes]
rs1624851	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414415	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2439045	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2439047	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2447712	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4144134	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs472579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774210	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774211	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774768	0.84[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs493968	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs501231	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]
rs549914	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]
rs593556	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs600753	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs60229152	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs606446	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs646322	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493789	0.89[ASN][1000 genomes]
rs6493791	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs685935	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs691447	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs692636	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7168202	0.91[ASN][1000 genomes]
rs7169179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7169948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7170993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174641	0.81[JPT][hapmap]
rs7174810	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8042996	0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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
13	nsv904244	chr15:55687969-55770911	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9920450	PIGB	cis	lymphoblastoid	seeQTL
rs9920450	PIGB	Cis_1M	lymphoblastoid	RTeQTL
rs9920450	TNFAIP8L3	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
2	chr15:55630000-55695000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:55637000-55699600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr15:55647800-55695400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:55649800-55695800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:55668200-55699800	Weak transcription	Spleen	Spleen
7	chr15:55670200-55695000	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:55671800-55695800	Weak transcription	HSMMtube	muscle
9	chr15:55672200-55696000	Weak transcription	Brain Substantia Nigra	brain
10	chr15:55676000-55695000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:55676000-55699400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:55676200-55695200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:55676200-55695800	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:55676400-55697200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:55676400-55699400	Weak transcription	Right Ventricle	heart
16	chr15:55676800-55695800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:55676800-55697600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:55677000-55695600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr15:55678200-55699400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:55679400-55696800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr15:55679600-55694400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:55679600-55695000	Weak transcription	Fetal Intestine Large	intestine
23	chr15:55681000-55695000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr15:55681000-55695800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:55681000-55697400	Weak transcription	Gastric	stomach
26	chr15:55681000-55699200	Weak transcription	Lung	lung
27	chr15:55681000-55699600	Weak transcription	Fetal Stomach	stomach
28	chr15:55681200-55693800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr15:55681200-55694000	Weak transcription	Liver	Liver
30	chr15:55681200-55694200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:55681200-55694400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:55681200-55695000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:55681200-55695600	Weak transcription	Fetal Intestine Small	intestine
34	chr15:55681200-55699400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr15:55681400-55695800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:55681600-55695600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr15:55681800-55695200	Weak transcription	Stomach Mucosa	stomach
38	chr15:55681800-55699600	Weak transcription	NHLF	lung
39	chr15:55682600-55695200	Weak transcription	Primary T cells from cord blood	blood
40	chr15:55687400-55695200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:55687400-55696800	Weak transcription	Psoas Muscle	Psoas
42	chr15:55687400-55699400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:55687400-55699400	Weak transcription	Fetal Brain Female	brain
44	chr15:55687400-55699600	Weak transcription	Left Ventricle	heart
45	chr15:55687800-55694800	Weak transcription	Primary B cells from cord blood	blood
46	chr15:55688000-55693800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr15:55688000-55694000	Weak transcription	Hela-S3	cervix
48	chr15:55689000-55693600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:55689000-55694200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:55689000-55694400	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links