Variant report

Variant	rs7348188
Chromosome Location	chr20:1098954-1098955
allele	C/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	CTCF	chr20:1098910-1099293	GM12878	blood:	n/a	n/a
2	MBD4	chr20:1098716-1099581	HepG2	liver:	n/a	n/a
3	TCF12	chr20:1098640-1099725	A549	lung:	n/a	n/a
4	POLR2A	chr20:1098596-1099519	K562	blood:	n/a	n/a
5	SIN3AK20	chr20:1098867-1099621	MCF-7	breast:	n/a	n/a
6	POU2F2	chr20:1098838-1099536	GM12878	blood:	n/a	n/a
7	FOSL2	chr20:1098829-1099719	HepG2	liver:	n/a	n/a
8	PBX3	chr20:1098890-1099456	SK-N-SH	brain:	n/a	n/a
9	YY1	chr20:1098804-1099919	HepG2	liver:	n/a	chr20:1099273-1099285
10	CHD2	chr20:1098858-1099428	H1-hESC	embryonic stem cell:	n/a	n/a
11	TBP	chr20:1098812-1099396	Hela-S3	cervix:	n/a	n/a
12	JUND	chr20:1098762-1099593	H1-hESC	embryonic stem cell:	n/a	n/a
13	YY1	chr20:1098855-1099596	K562	blood:	n/a	chr20:1099273-1099285
14	TAF1	chr20:1098927-1099407	SK-N-SH	brain:	n/a	n/a
15	RCOR1	chr20:1098885-1099420	GM12878	blood:	n/a	n/a
16	POLR2A	chr20:1098785-1099566	HCT-116	colon:	n/a	n/a
17	ELF1	chr20:1098818-1099445	A549	lung:	n/a	chr20:1099125-1099134 chr20:1099238-1099249 chr20:1099123-1099136 chr20:1099239-1099248
18	RCOR1	chr20:1098654-1099436	K562	blood:	n/a	n/a
19	TEAD4	chr20:1098631-1099285	K562	blood:	n/a	n/a
20	POLR2A	chr20:1098649-1099800	PFSK-1	brain:	n/a	n/a
21	USF1	chr20:1098913-1099295	K562	blood:	n/a	n/a
22	TAF1	chr20:1098838-1099535	GM12878	blood:	n/a	n/a
23	ELK1	chr20:1098902-1099381	Hela-S3	cervix:	n/a	chr20:1099238-1099247 chr20:1099238-1099247
24	MAX	chr20:1098865-1099663	K562	blood:	n/a	n/a
25	RUNX3	chr20:1098873-1099784	GM12878	blood:	n/a	n/a
26	MXI1	chr20:1098570-1100368	IMR90	lung:	n/a	n/a
27	SP1	chr20:1098653-1099600	A549	lung:	n/a	chr20:1098999-1099013 chr20:1099566-1099580 chr20:1099142-1099152
28	TEAD4	chr20:1098855-1099337	H1-hESC	embryonic stem cell:	n/a	n/a
29	JUN	chr20:1098617-1099722	K562	blood:	n/a	n/a
30	POLR2A	chr20:1098865-1099587	A549	lung:	n/a	n/a
31	IRF1	chr20:1098734-1099989	K562	blood:	n/a	chr20:1099139-1099153
32	POLR2A	chr20:1098611-1099978	GM12878	blood:	n/a	n/a
33	POLR2A	chr20:1098833-1099724	GM15510	blood:	n/a	n/a
34	EP300	chr20:1098812-1099557	A549	lung:	n/a	chr20:1099239-1099246 chr20:1099153-1099166
35	POLR2A	chr20:1098837-1099527	K562	blood:	n/a	n/a
36	YY1	chr20:1098842-1099633	SK-N-SH_RA	brain:	n/a	chr20:1099273-1099285
37	FOXA1	chr20:1098858-1099550	HepG2	liver:	n/a	n/a
38	FOXM1	chr20:1098845-1099291	GM12878	blood:	n/a	n/a
39	ELF1	chr20:1098700-1099571	HepG2	liver:	n/a	chr20:1099125-1099134 chr20:1099238-1099249 chr20:1099123-1099136 chr20:1099239-1099248
40	POLR2A	chr20:1098476-1101083	HepG2	liver:	n/a	n/a
41	CEBPD	chr20:1098875-1099330	K562	blood:	n/a	n/a
42	ZNF263	chr20:1098795-1099530	HEK293-T-REx	kidney:	n/a	n/a
43	PML	chr20:1098902-1099533	MCF-7	breast:	n/a	n/a
44	YY1	chr20:1098829-1099772	ECC-1	luminal epithelium:	n/a	chr20:1099273-1099285
45	SIN3AK20	chr20:1098913-1099788	H1-hESC	embryonic stem cell:	n/a	n/a
46	GABPA	chr20:1098866-1099651	MCF-7	breast:	n/a	n/a
47	POLR2A	chr20:1098865-1099573	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr20:1098786-1099560	SK-N-SH	brain:	n/a	n/a
49	GABPA	chr20:1098836-1099712	K562	blood:	n/a	n/a
50	SIN3AK20	chr20:1098833-1099396	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:1087941..1090289-chr20:1097443..1099085,2	K562	blood:
2	chr16:3109089..3109876-chr20:1098820..1099738,2	HCT-116	colon:
3	chr15:65596673..65597233-chr20:1098833..1099436,3	NB4	blood:
4	chr20:1093479..1095284-chr20:1095646..1099615,3	K562	blood:
5	chr11:67159204..67159871-chr20:1098628..1099177,2	NB4	blood:

Variant related genes	Relation type
PSMF1	TF binding region
ENSG00000125818	Chromatin interaction
ENSG00000172613	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000261971	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11087015	0.97[ASN][1000 genomes]
rs11696399	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11696575	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11696674	0.92[EUR][1000 genomes]
rs11697070	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11699188	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11699627	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11699981	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3787573	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs45443791	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4553882	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6032877	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6032895	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6032947	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs6039915	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6039922	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6039940	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6040044	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6040122	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60728448	0.97[ASN][1000 genomes]
rs6514113	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6514115	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73071630	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8117499	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv531450	chr20:809607-1221836	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1058524	chr20:821434-1254865	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544138	chr20:821434-1254865	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1065838	chr20:866302-1147601	Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544139	chr20:866302-1147601	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1055328	chr20:867911-1145765	Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1059611	chr20:867911-1158694	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv544140	chr20:867911-1158694	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv949356	chr20:961527-1135413	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912585	chr20:992713-1210647	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	esv1799982	chr20:1097289-1136252	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7348188	PSMF1	cis	Esophagus Muscularis	GTEx
rs7348188	PSMF1	cis	Nerve Tibial	GTEx
rs7348188	PSMF1	cis	Artery Tibial	GTEx
rs7348188	PSMF1	Cis_1M	lymphoblastoid	RTeQTL
rs7348188	PSMF1	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1098200-1099000	Enhancers	Spleen	Spleen
2	chr20:1098200-1099000	Flanking Active TSS	Dnd41	blood
3	chr20:1098200-1100000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr20:1098400-1099000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr20:1098400-1099000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr20:1098400-1099000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr20:1098400-1099000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr20:1098400-1099000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr20:1098400-1099000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr20:1098400-1099000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr20:1098400-1099000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr20:1098400-1099000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr20:1098400-1099000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr20:1098400-1099000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr20:1098400-1099000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr20:1098400-1099000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr20:1098400-1099000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr20:1098400-1099000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr20:1098400-1099000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr20:1098400-1099000	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr20:1098400-1099000	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr20:1098400-1099000	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr20:1098400-1099000	Flanking Active TSS	Fetal Brain Male	brain
24	chr20:1098400-1099000	Flanking Active TSS	Fetal Brain Female	brain
25	chr20:1098400-1099000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr20:1098400-1099000	Flanking Active TSS	GM12878-XiMat	blood
27	chr20:1098400-1099000	Flanking Active TSS	Hela-S3	cervix
28	chr20:1098400-1099000	Flanking Active TSS	HMEC	breast
29	chr20:1098400-1099000	Flanking Active TSS	NHEK	skin
30	chr20:1098400-1099600	Active TSS	Colonic Mucosa	Colon
31	chr20:1098400-1099800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr20:1098400-1099800	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr20:1098400-1099800	Active TSS	Rectal Smooth Muscle	rectum
34	chr20:1098400-1100000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr20:1098400-1100000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr20:1098400-1100000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr20:1098400-1100000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr20:1098400-1100000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr20:1098400-1100200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr20:1098400-1100400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr20:1098400-1101000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr20:1098600-1099000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
43	chr20:1098600-1099000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr20:1098600-1099000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr20:1098600-1099000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr20:1098600-1099000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr20:1098600-1099000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr20:1098600-1099000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr20:1098600-1099000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr20:1098600-1099000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links