Variant report

Variant	rs12963761
Chromosome Location	chr18:12306995-12306996
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:12304971-12316847	IMR90	lung:	n/a	n/a
2	CHD1	chr18:12306712-12310268	IMR90	lung:	n/a	chr18:12307601-12307611
3	MAZ	chr18:12306781-12309329	IMR90	lung:	n/a	chr18:12308001-12308011
4	POLR2A	chr18:12306708-12310326	U87	brain:	n/a	n/a
5	CTBP2	chr18:12306327-12308033	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr18:12306468-12307015	IMR90	lung:	n/a	n/a
7	JUND	chr18:12306818-12307018	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12305136..12307294-chr18:12373188..12375992,2	K562	blood:
2	chr18:12305088..12307512-chr18:12313207..12314857,2	MCF-7	breast:
3	chr18:12306558..12308875-chr18:12376128..12379112,4	MCF-7	breast:
4	chr18:12306506..12308836-chr18:12701681..12703824,3	K562	blood:
5	chr18:12306891..12312604-chr18:12376208..12378768,5	K562	blood:
6	chr18:12305251..12310573-chr18:12373540..12378768,12	K562	blood:
7	chr18:12305189..12307531-chr18:12348513..12350554,2	K562	blood:

No data

Variant related genes	Relation type
TUBB6	TF binding region
RNU6-170P	TF binding region
ENSG00000128789	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000101624	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10853224	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11080567	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11267036	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11548177	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11659246	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11660106	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11660222	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11663340	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11664255	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11664282	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12455756	0.88[EUR][1000 genomes]
rs12607250	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12607321	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12607378	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12954560	0.86[EUR][1000 genomes]
rs12959653	0.82[ASN][1000 genomes]
rs12959674	0.89[ASN][1000 genomes]
rs12960267	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12965912	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12970667	0.91[ASN][1000 genomes]
rs28625182	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34685983	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35242253	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796958	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796959	0.91[ASN][1000 genomes]
rs4796960	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796962	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4796963	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4797672	0.83[ASN][1000 genomes]
rs4797673	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4797674	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4797675	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58136410	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61604633	0.89[EUR][1000 genomes]
rs62097556	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505749	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505751	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7231304	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7233290	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7244254	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7244709	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7504558	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7504575	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7504616	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7505208	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7505255	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7505626	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8083882	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8087843	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8098040	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8098700	0.81[ASN][1000 genomes]
rs8099636	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9303766	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9303767	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9303768	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9652931	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9807444	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9945901	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9946172	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9946217	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9946347	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9949054	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9954945	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9958069	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9958525	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9964163	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9966470	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv909401	chr18:12211483-12312075	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
6	nsv909403	chr18:12231060-12325222	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1061545	chr18:12235999-12328405	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv1058661	chr18:12280366-12313865	Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12963761	TUBB6	cis	multi-tissue	Pritchard
rs12963761	TUBB6	Cis_1M	lymphoblastoid	RTeQTL
rs12963761	TUBB6	cis	Whole Blood	GTEx
rs12963761	MC1R///TUBB3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12304600-12307000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr18:12304600-12307000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:12305200-12307200	Enhancers	Fetal Heart	heart
4	chr18:12305200-12307200	Enhancers	Right Ventricle	heart
5	chr18:12305600-12307000	Weak transcription	NHEK	skin
6	chr18:12305600-12307800	Weak transcription	Pancreas	Pancrea
7	chr18:12306000-12307000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
8	chr18:12306000-12307000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr18:12306000-12307000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr18:12306000-12307200	Enhancers	Placenta	Placenta
11	chr18:12306000-12307600	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr18:12306200-12307000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr18:12306200-12307000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
14	chr18:12306200-12307000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
15	chr18:12306200-12307000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr18:12306200-12307000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
17	chr18:12306200-12307000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr18:12306200-12307000	Flanking Bivalent TSS/Enh	HepG2	liver
19	chr18:12306200-12307200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr18:12306200-12307200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:12306200-12307200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr18:12306200-12307200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
23	chr18:12306200-12307400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
24	chr18:12306200-12307400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
25	chr18:12306200-12307400	Flanking Active TSS	NH-A	brain
26	chr18:12306400-12307000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr18:12306400-12307000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
28	chr18:12306400-12307000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr18:12306400-12307000	Enhancers	Ovary	ovary
30	chr18:12306400-12307000	Flanking Active TSS	Rectal Smooth Muscle	rectum
31	chr18:12306400-12307000	Flanking Active TSS	HSMM	muscle
32	chr18:12306400-12307000	Flanking Active TSS	NHLF	lung
33	chr18:12306400-12307200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr18:12306400-12307200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr18:12306400-12307200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr18:12306400-12307200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
37	chr18:12306400-12307600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr18:12306400-12307600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
39	chr18:12306400-12308000	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr18:12306400-12309400	Active TSS	HSMMtube	muscle
41	chr18:12306600-12307000	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
42	chr18:12306600-12307000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
43	chr18:12306600-12307000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr18:12306600-12307000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr18:12306600-12307000	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr18:12306600-12307000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr18:12306600-12307000	Weak transcription	Esophagus	oesophagus
48	chr18:12306600-12307000	Flanking Active TSS	NHDF-Ad	bronchial
49	chr18:12306600-12307000	Flanking Active TSS	Osteobl	bone
50	chr18:12306600-12307200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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