Variant report

Variant	rs6074148
Chromosome Location	chr20:1098486-1098487
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	chr20:1098476-1101083	HepG2	liver:	n/a	n/a
2	MXI1	chr20:1098217-1100198	SK-N-SH	brain:	n/a	n/a
3	ESRRA	chr20:1098352-1099804	GM12878	blood:	n/a	chr20:1099721-1099734
4	POLR2A	chr20:1098457-1100420	GM12878	blood:	n/a	n/a
5	REST	chr20:1098374-1099900	H1-neurons	neurons:	n/a	chr20:1099077-1099084
6	POLR2A	chr20:1097775-1099943	K562	blood:	n/a	n/a
7	MYC	chr20:1098486-1100584	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1087941..1090289-chr20:1097443..1099085,2	K562	blood:
2	chr20:1093479..1095284-chr20:1095646..1099615,3	K562	blood:

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

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1803415	0.88[GIH][hapmap];0.90[JPT][hapmap]
rs1883522	0.86[JPT][hapmap]
rs2072961	0.90[JPT][hapmap]
rs2072962	0.95[JPT][hapmap]
rs2072963	0.90[JPT][hapmap]
rs2072964	0.95[JPT][hapmap]
rs2179449	0.86[JPT][hapmap]
rs2179450	0.86[JPT][hapmap]
rs2235587	0.81[JPT][hapmap]
rs2268065	0.88[GIH][hapmap];0.90[JPT][hapmap]
rs2284371	0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2284372	0.88[GIH][hapmap];0.90[JPT][hapmap]
rs3787572	0.90[JPT][hapmap]
rs4289256	0.88[GIH][hapmap];0.90[JPT][hapmap]
rs4813030	0.85[YRI][hapmap]
rs6040024	0.90[JPT][hapmap]
rs6040066	0.88[GIH][hapmap];0.90[JPT][hapmap]
rs6077826	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6077915	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs6133957	0.90[JPT][hapmap]
rs6133961	0.90[JPT][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6074148	PSMF1	cis	parietal	SCAN
rs6074148	MAVS	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1095000-1098600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr20:1095000-1098600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr20:1095200-1098600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr20:1096200-1098600	Weak transcription	Gastric	stomach
5	chr20:1096200-1098600	Weak transcription	Stomach Mucosa	stomach
6	chr20:1097800-1098600	Enhancers	Pancreas	Pancrea
7	chr20:1098200-1098600	Enhancers	Primary B cells from peripheral blood	blood
8	chr20:1098200-1098600	Enhancers	Primary T cells fromperipheralblood	blood
9	chr20:1098200-1098600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr20:1098200-1098600	Enhancers	Aorta	Aorta
11	chr20:1098200-1098600	Enhancers	Fetal Kidney	kidney
12	chr20:1098200-1098600	Enhancers	Fetal Muscle Leg	muscle
13	chr20:1098200-1098600	Active TSS	HSMM	muscle
14	chr20:1098200-1099000	Enhancers	Spleen	Spleen
15	chr20:1098200-1099000	Flanking Active TSS	Dnd41	blood
16	chr20:1098200-1100000	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr20:1098400-1098600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr20:1098400-1098600	Enhancers	H9 Cell Line	embryonic stem cell
19	chr20:1098400-1098600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr20:1098400-1098600	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr20:1098400-1098600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr20:1098400-1098600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr20:1098400-1098600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr20:1098400-1098600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr20:1098400-1098600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr20:1098400-1098600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr20:1098400-1098600	Enhancers	Primary B cells from cord blood	blood
28	chr20:1098400-1098600	Active TSS	Primary T cells from cord blood	blood
29	chr20:1098400-1098600	Enhancers	Primary hematopoietic stem cells	blood
30	chr20:1098400-1098600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr20:1098400-1098600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr20:1098400-1098600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr20:1098400-1098600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr20:1098400-1098600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr20:1098400-1098600	Enhancers	Liver	Liver
36	chr20:1098400-1098600	Enhancers	Brain Angular Gyrus	brain
37	chr20:1098400-1098600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr20:1098400-1098600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr20:1098400-1098600	Enhancers	Fetal Heart	heart
40	chr20:1098400-1098600	Enhancers	Fetal Intestine Large	intestine
41	chr20:1098400-1098600	Enhancers	Fetal Intestine Small	intestine
42	chr20:1098400-1098600	Enhancers	Fetal Thymus	thymus
43	chr20:1098400-1098600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr20:1098400-1098600	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr20:1098400-1098600	Enhancers	Right Ventricle	heart
46	chr20:1098400-1098600	Enhancers	Thymus	Thymus
47	chr20:1098400-1098600	Enhancers	HUVEC	blood vessel
48	chr20:1098400-1098600	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr20:1098400-1098600	Enhancers	NH-A	brain
50	chr20:1098400-1098600	Active TSS	NHDF-Ad	bronchial

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