Variant report

Variant	rs9956171
Chromosome Location	chr18:12362952-12362953
allele	A/C
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	chr18:12362380-12363140	K562	blood:	n/a	n/a
2	CEBPB	chr18:12362895-12363123	HepG2	liver:	n/a	chr18:12362969-12362980
3	MAFK	chr18:12362920-12363224	HepG2	liver:	n/a	chr18:12363070-12363081 chr18:12363070-12363086 chr18:12363071-12363082 chr18:12363070-12363081 chr18:12363070-12363085
4	MAFK	chr18:12362932-12363227	HepG2	liver:	n/a	chr18:12363070-12363081 chr18:12363070-12363086 chr18:12363071-12363082 chr18:12363070-12363081 chr18:12363070-12363085
5	MAFF	chr18:12362911-12363215	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12362548..12366829-chr18:12375336..12378234,6	MCF-7	breast:
2	chr18:12361542..12363556-chr18:12365660..12367206,2	K562	blood:
3	chr18:12361778..12363589-chr18:12374955..12376889,2	K562	blood:
4	chr18:12360642..12363502-chr18:12370085..12373310,4	K562	blood:
5	chr18:12336416..12339580-chr18:12362136..12364689,3	K562	blood:
6	chr18:12362726..12365078-chr18:12367506..12369159,2	MCF-7	breast:
7	chr18:12361813..12363369-chr18:12375355..12378184,2	MCF-7	breast:
8	chr18:12360702..12363372-chr18:12365362..12368276,3	MCF-7	breast:

Variant related genes	Relation type
AFG3L2	TF binding region
ENSG00000141385	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10853225	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11080564	0.80[CEU][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs11080571	0.85[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs11080572	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1129115	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs11553521	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11662523	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11664216	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11875938	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12455273	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12456857	0.80[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs12604732	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12968089	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12968566	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1547858	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1941222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2003881	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298542	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2509510	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28372882	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35968035	0.88[ASN][1000 genomes]
rs3786260	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs478088	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4797677	0.80[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4797680	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs553091	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs566960	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs693449	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7231182	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7231409	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7235237	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7235296	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7407640	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7504908	0.85[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs7504974	0.85[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs7505834	0.80[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap]
rs8086993	0.97[GIH][hapmap]
rs8092506	0.80[CEU][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]
rs8093375	0.95[CEU][hapmap]
rs8097342	0.85[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9303769	0.85[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9303770	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs9303771	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9635829	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9960103	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9964406	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers 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	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9956171	TUBB6	cis	Whole Blood	GTEx
rs9956171	TUBB6	cis	lymphoblastoid	seeQTL
rs9956171	TUBB6	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12326200-12366400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr18:12333200-12370800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr18:12333200-12371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr18:12333400-12366600	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr18:12333400-12370200	Strong transcription	Fetal Thymus	thymus
6	chr18:12333400-12370800	Strong transcription	Fetal Muscle Leg	muscle
7	chr18:12333400-12371400	Strong transcription	Fetal Stomach	stomach
8	chr18:12333600-12364000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr18:12333600-12366400	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr18:12333600-12369600	Strong transcription	Placenta	Placenta
11	chr18:12333600-12369800	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr18:12333800-12369400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr18:12334000-12369400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr18:12337000-12367600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr18:12337000-12374200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr18:12337200-12369400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr18:12337400-12369800	Strong transcription	Liver	Liver
18	chr18:12337400-12370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr18:12337800-12369600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr18:12337800-12370800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:12339200-12368800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr18:12339800-12370200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr18:12339800-12371400	Strong transcription	Dnd41	blood
24	chr18:12340000-12365000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr18:12340000-12369400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr18:12340000-12369400	Strong transcription	HepG2	liver
27	chr18:12340000-12369600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr18:12340000-12370800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr18:12340000-12371400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr18:12340000-12371600	Strong transcription	GM12878-XiMat	blood
31	chr18:12340200-12366400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr18:12340200-12369400	Strong transcription	Hela-S3	cervix
33	chr18:12340400-12367400	Strong transcription	Thymus	Thymus
34	chr18:12341000-12370800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr18:12341000-12370800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr18:12341000-12370800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr18:12341600-12369400	Strong transcription	Lung	lung
38	chr18:12341600-12370800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr18:12341800-12369400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr18:12349200-12369400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr18:12349600-12366000	Strong transcription	Fetal Intestine Small	intestine
42	chr18:12350600-12369600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr18:12353600-12369600	Strong transcription	Primary B cells from cord blood	blood
44	chr18:12354200-12369400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr18:12355200-12367600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr18:12355400-12367800	Strong transcription	HMEC	breast
47	chr18:12355400-12369400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr18:12356800-12369000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr18:12357800-12363200	Strong transcription	Gastric	stomach
50	chr18:12357800-12367800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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