Variant report

Variant	rs6133957
Chromosome Location	chr20:1104013-1104014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1102002..1104790-chr20:1105362..1109847,4	MCF-7	breast:
2	chr20:1102460..1104842-chr20:1112243..1114796,2	K562	blood:
3	chr20:1099357..1100931-chr20:1102003..1104319,2	K562	blood:
4	chr20:1097920..1101650-chr20:1101815..1104250,4	MCF-7	breast:
5	chr20:1102674..1104327-chr20:1107273..1110079,2	K562	blood:
6	chr20:1098005..1100857-chr20:1102003..1104292,3	K562	blood:

Variant related genes	Relation type
ENSG00000125818	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11908561	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16991645	0.81[AMR][1000 genomes]
rs1803415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883522	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs2072961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072962	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072963	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072964	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2179450	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs2235587	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2268065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284371	0.91[JPT][hapmap]
rs2284372	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142353	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4289256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4813923	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6040009	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040024	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6040108	0.86[ASN][1000 genomes]
rs6040155	0.80[JPT][hapmap]
rs6074148	0.90[JPT][hapmap]
rs6077826	0.90[JPT][hapmap]
rs6077915	0.81[JPT][hapmap]
rs6133961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6133989	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6133957	ProSAPiP1	cis	parietal	SCAN
rs6133957	PSMF1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1100200-1105800	Weak transcription	Aorta	Aorta
2	chr20:1100200-1106200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:1100400-1104200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr20:1100400-1105800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr20:1100400-1106200	Weak transcription	HSMMtube	muscle
6	chr20:1100400-1115200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr20:1100400-1132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr20:1100400-1146600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr20:1100600-1104400	Enhancers	Stomach Mucosa	stomach
10	chr20:1100600-1104600	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr20:1100600-1105200	Enhancers	Psoas Muscle	Psoas
12	chr20:1100600-1105800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr20:1100600-1105800	Weak transcription	Esophagus	oesophagus
14	chr20:1100600-1106000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr20:1100800-1104200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr20:1100800-1104600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr20:1100800-1106400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr20:1100800-1122200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr20:1101000-1104400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr20:1101000-1105800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr20:1101000-1105800	Weak transcription	Fetal Kidney	kidney
22	chr20:1101200-1105800	Weak transcription	Colonic Mucosa	Colon
23	chr20:1101200-1105800	Weak transcription	NH-A	brain
24	chr20:1101400-1104200	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr20:1101400-1105400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
26	chr20:1101600-1104400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr20:1101600-1104400	Weak transcription	Hela-S3	cervix
28	chr20:1101600-1104600	Enhancers	Left Ventricle	heart
29	chr20:1101600-1104600	Genic enhancers	Dnd41	blood
30	chr20:1101600-1105200	Enhancers	Brain Cingulate Gyrus	brain
31	chr20:1101600-1105800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr20:1101600-1105800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr20:1101600-1105800	Weak transcription	Spleen	Spleen
34	chr20:1101800-1104800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr20:1101800-1105600	Weak transcription	HSMM	muscle
36	chr20:1101800-1105800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr20:1101800-1111600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr20:1102200-1104600	Enhancers	Small Intestine	intestine
39	chr20:1102200-1105200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr20:1102200-1105400	Weak transcription	Fetal Intestine Large	intestine
41	chr20:1102200-1105600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr20:1102200-1105800	Weak transcription	Fetal Brain Female	brain
43	chr20:1102200-1106000	Weak transcription	Gastric	stomach
44	chr20:1102200-1106200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr20:1102200-1107600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr20:1102200-1128600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr20:1102400-1104600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr20:1102600-1104600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr20:1102600-1105800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr20:1102600-1111200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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