Variant report

Variant	rs62098961
Chromosome Location	chr18:12307970-12307971
allele	G/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	MAX	chr18:12307154-12308384	NB4	blood:	n/a	chr18:12308001-12308011
2	SIN3A	chr18:12307178-12309035	H1-hESC	embryonic stem cell:	n/a	chr18:12308357-12308370
3	CTCF	chr18:12307940-12308090	SAEC	small airway:	n/a	chr18:12307978-12307991
4	CTCF	chr18:12307900-12308050	AG10803	skin:	n/a	chr18:12307978-12307991
5	CTCF	chr18:12307920-12308070	HUVEC	blood vessel:	n/a	chr18:12307978-12307991
6	CTCF	chr18:12307920-12308070	HBMEC	blood vessel:	n/a	chr18:12307978-12307991
7	POLR2A	chr18:12307748-12308946	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr18:12307838-12308852	PANC-1	pancreas:	n/a	n/a
9	YY1	chr18:12307875-12308481	GM12891	blood:	n/a	chr18:12307927-12307938
10	MAX	chr18:12307829-12309191	A549	lung:	n/a	chr18:12308001-12308011
11	POLR2A	chr18:12307196-12309126	ProgFib	skin:	n/a	n/a
12	CTCF	chr18:12307940-12308090	AG04449	skin:	n/a	chr18:12307978-12307991
13	POLR2A	chr18:12307888-12308975	HEK293	kidney:	n/a	n/a
14	MAX	chr18:12307809-12308503	H1-hESC	embryonic stem cell:	n/a	chr18:12308001-12308011
15	EGR1	chr18:12307899-12308435	ECC-1	luminal epithelium:	n/a	chr18:12308094-12308103 chr18:12308141-12308155 chr18:12308001-12308011 chr18:12308280-12308290 chr18:12307998-12308011
16	POLR2A	chr18:12307140-12311108	MCF10A-Er-Src	breast:	n/a	n/a
17	CHD2	chr18:12307940-12308051	GM12878	blood:	n/a	n/a
18	POLR2A	chr18:12307869-12309146	SK-N-SH	brain:	n/a	n/a
19	YY1	chr18:12307919-12308545	GM12892	blood:	n/a	chr18:12307927-12307938
20	POLR2A	chr18:12307792-12309181	GM12878	blood:	n/a	n/a
21	JUND	chr18:12307075-12309165	SK-N-SH	brain:	n/a	chr18:12307795-12307804 chr18:12308781-12308792
22	CTCF	chr18:12307900-12308050	HVMF	connective:	n/a	chr18:12307978-12307991
23	YY1	chr18:12307899-12308620	HepG2	liver:	n/a	chr18:12307927-12307938 chr18:12308538-12308549 chr18:12308563-12308577
24	CTCF	chr18:12307900-12308050	AG09319	gingival:	n/a	chr18:12307978-12307991
25	ZBTB7A	chr18:12307717-12309262	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr18:12307816-12309201	ECC-1	luminal epithelium:	n/a	n/a
27	TAF1	chr18:12307929-12308446	GM12878	blood:	n/a	n/a
28	RAD21	chr18:12307840-12308503	H1-hESC	embryonic stem cell:	n/a	chr18:12308037-12308051 chr18:12308039-12308053
29	THAP1	chr18:12307870-12308147	K562	blood:	n/a	n/a
30	POLR2A	chr18:12304971-12316847	IMR90	lung:	n/a	n/a
31	TAF1	chr18:12307949-12308487	PFSK-1	brain:	n/a	n/a
32	ZNF143	chr18:12307358-12308916	GM12878	blood:	n/a	chr18:12308007-12308017 chr18:12308280-12308290 chr18:12307625-12307635
33	POLR2A	chr18:12307791-12309161	GM12878	blood:	n/a	n/a
34	EGR1	chr18:12307847-12308406	ECC-1	luminal epithelium:	n/a	chr18:12308094-12308103 chr18:12308141-12308155 chr18:12308001-12308011 chr18:12308280-12308290 chr18:12307998-12308011
35	SIN3AK20	chr18:12307911-12309062	HCT-116	colon:	n/a	n/a
36	POLR2A	chr18:12307789-12309217	U87	brain:	n/a	n/a
37	TBP	chr18:12307908-12309140	K562	blood:	n/a	n/a
38	POLR2A	chr18:12307827-12309066	K562	blood:	n/a	n/a
39	CTCF	chr18:12307920-12308070	SK-N-SH_RA	brain:	n/a	chr18:12307978-12307991
40	CHD1	chr18:12306712-12310268	IMR90	lung:	n/a	chr18:12307601-12307611
41	CTCF	chr18:12307920-12308070	AoAF	blood vessel:	n/a	chr18:12307978-12307991
42	CTCF	chr18:12307920-12308070	HMF	breast:	n/a	chr18:12307978-12307991
43	CTCF	chr18:12307940-12308090	HEK293	kidney:	n/a	chr18:12307978-12307991
44	POLR2A	chr18:12307891-12308145	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr18:12307879-12309131	GM19193	blood:	n/a	n/a
46	TAF1	chr18:12307923-12308636	ECC-1	luminal epithelium:	n/a	n/a
47	TAF1	chr18:12307934-12309159	K562	blood:	n/a	n/a
48	CTCF	chr18:12307895-12308048	Lung_OC	lung:	n/a	chr18:12307978-12307991
49	E2F6	chr18:12307933-12309059	K562	blood:	n/a	chr18:12308938-12308945 chr18:12308007-12308017 chr18:12308281-12308290 chr18:12308003-12308012 chr18:12308604-12308614 chr18:12308938-12308945 chr18:12308934-12308946 chr18:12308937-12308946 chr18:12308938-12308945
50	CTCF	chr18:12307891-12308075	NHEK	skin:	n/a	chr18:12307978-12307991

No.	Distal block	Cell Line	Cell type
1	chr18:12307823..12308792-chr7:152160863..152161673,3	Hela-S3	cervix:
2	chr18:12307735..12310451-chr18:12655693..12658579,2	MCF-7	breast:
3	chr18:12306558..12308875-chr18:12376128..12379112,4	MCF-7	breast:
4	chr18:12307737..12309568-chr20:45947449..45950208,2	MCF-7	breast:
5	chr18:12307367..12309512-chr18:12310463..12312362,3	MCF-7	breast:
6	chr18:12307184..12308743-chr18:12701040..12703824,2	K562	blood:
7	chr18:12306506..12308836-chr18:12701681..12703824,3	K562	blood:
8	chr18:12307869..12309956-chr18:12375801..12377728,3	MCF-7	breast:
9	chr18:12306891..12312604-chr18:12376208..12378768,5	K562	blood:
10	chr18:12305251..12310573-chr18:12373540..12378768,12	K562	blood:
11	chr18:12303398..12305461-chr18:12307257..12308973,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-170P	TF binding region
TUBB6	TF binding region
ENSG00000176014	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000199702	Chromatin interaction
ENSG00000261455	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000134278	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10459999	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10460000	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10460001	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11080564	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11080565	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11080569	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11080571	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1129115	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11665134	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12455770	0.81[EUR][1000 genomes]
rs12456857	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12604732	0.81[AMR][1000 genomes]
rs12954686	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12968566	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34829762	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35338639	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4796961	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4796964	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7504908	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7504974	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7505834	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8086821	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8086993	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8087840	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8092506	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9946698	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9951945	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
13	esv3316265	chr18:12307177-12309725	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
14	esv3316266	chr18:12307177-12309725	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
15	esv3345228	chr18:12307452-12309350	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62098961	TUBB6	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12306400-12308000	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr18:12306400-12309400	Active TSS	HSMMtube	muscle
3	chr18:12306600-12309600	Active TSS	Right Atrium	heart
4	chr18:12306800-12308000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
5	chr18:12306800-12308600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
6	chr18:12307000-12308000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr18:12307000-12308000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
8	chr18:12307000-12308800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr18:12307000-12309000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr18:12307000-12309400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr18:12307000-12309400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr18:12307000-12309400	Active TSS	Ovary	ovary
13	chr18:12307000-12309400	Active TSS	HSMM	muscle
14	chr18:12307000-12309400	Active TSS	NHDF-Ad	bronchial
15	chr18:12307000-12309400	Active TSS	NHLF	lung
16	chr18:12307000-12309600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr18:12307000-12309600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr18:12307000-12309600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr18:12307000-12309600	Active TSS	Colon Smooth Muscle	Colon
20	chr18:12307000-12309600	Active TSS	Rectal Smooth Muscle	rectum
21	chr18:12307000-12309800	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr18:12307200-12308000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
23	chr18:12307200-12308000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
24	chr18:12307200-12308200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr18:12307200-12308800	Active TSS	Muscle Satellite Cultured Cells	--
26	chr18:12307200-12308800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr18:12307200-12308800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
28	chr18:12307200-12308800	Bivalent/Poised TSS	Fetal Brain Female	brain
29	chr18:12307200-12308800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
30	chr18:12307200-12309000	Active TSS	Lung	lung
31	chr18:12307200-12309000	Active TSS	Small Intestine	intestine
32	chr18:12307200-12309200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr18:12307200-12309200	Bivalent/Poised TSS	Thymus	Thymus
34	chr18:12307200-12309400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr18:12307200-12309400	Bivalent/Poised TSS	Fetal Lung	lung
36	chr18:12307200-12309400	Active TSS	Hela-S3	cervix
37	chr18:12307200-12309600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr18:12307200-12309600	Active TSS	Left Ventricle	heart
39	chr18:12307200-12309800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr18:12307200-12310000	Active TSS	Aorta	Aorta
41	chr18:12307400-12308000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr18:12307400-12308000	Bivalent Enhancer	Fetal Brain Male	brain
43	chr18:12307400-12308200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr18:12307400-12308200	Weak transcription	Spleen	Spleen
45	chr18:12307400-12308400	Bivalent/Poised TSS	Colonic Mucosa	Colon
46	chr18:12307400-12308400	Active TSS	Psoas Muscle	Psoas
47	chr18:12307400-12308400	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
48	chr18:12307400-12308800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr18:12307400-12309000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr18:12307400-12309000	Active TSS	Fetal Stomach	stomach

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