Variant report

Variant	rs1547180
Chromosome Location	chr1:46768408-46768409
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	TAF1	chr1:46767236-46769829	K562	blood:	n/a	n/a
2	TAF1	chr1:46768322-46768605	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr1:46767384-46769729	ECC-1	luminal epithelium:	n/a	n/a
4	STAT5A	chr1:46767420-46769682	GM12878	blood:	n/a	chr1:46769109-46769123 chr1:46768216-46768228
5	SIN3AK20	chr1:46768355-46769849	SK-N-SH	brain:	n/a	n/a
6	YY1	chr1:46768256-46769719	GM12878	blood:	n/a	chr1:46769033-46769043 chr1:46769033-46769055 chr1:46769036-46769044 chr1:46769034-46769042 chr1:46768257-46768266
7	PML	chr1:46767513-46770040	GM12878	blood:	n/a	n/a
8	MTA3	chr1:46767583-46770112	GM12878	blood:	n/a	n/a
9	SIN3A	chr1:46767378-46770073	H1-hESC	embryonic stem cell:	n/a	chr1:46768489-46768500 chr1:46767692-46767705
10	TAF1	chr1:46767350-46769638	ECC-1	luminal epithelium:	n/a	n/a
11	ZBTB7A	chr1:46767349-46769086	K562	blood:	n/a	chr1:46767848-46767856 chr1:46768015-46768023 chr1:46767894-46767903
12	POLR2A	chr1:46767779-46770030	GM12878	blood:	n/a	n/a
13	MXI1	chr1:46768312-46769699	HepG2	liver:	n/a	n/a
14	SMARCB1	chr1:46767044-46769686	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:46768125-46768572	GM12891	blood:	n/a	n/a
16	ZNF263	chr1:46766530-46768622	HEK293-T-REx	kidney:	n/a	chr1:46766611-46766620
17	MYC	chr1:46767974-46769583	Hela-S3	cervix:	n/a	chr1:46769290-46769300 chr1:46768019-46768029
18	TAF1	chr1:46767310-46769072	HepG2	liver:	n/a	n/a
19	CHD2	chr1:46767772-46769562	GM12878	blood:	n/a	chr1:46768555-46768565 chr1:46768044-46768054
20	TAF1	chr1:46767593-46769841	H1-hESC	embryonic stem cell:	n/a	n/a
21	REST	chr1:46768387-46769801	HL-60	blood:	n/a	n/a
22	POLR2A	chr1:46767608-46770025	Raji	blood:	n/a	n/a
23	HEY1	chr1:46767177-46768463	K562	blood:	n/a	chr1:46767931-46767946 chr1:46767887-46767902 chr1:46767890-46767905
24	POLR2A	chr1:46766823-46769085	ECC-1	luminal epithelium:	n/a	n/a
25	YY1	chr1:46767228-46769657	HepG2	liver:	n/a	chr1:46767886-46767895 chr1:46769033-46769043 chr1:46767886-46767900 chr1:46769033-46769055 chr1:46768184-46768193 chr1:46767891-46767905 chr1:46769036-46769044 chr1:46767788-46767802 chr1:46769034-46769042 chr1:46768257-46768266
26	TBP	chr1:46768238-46768422	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr1:46767125-46769928	HepG2	liver:	n/a	n/a
28	E2F6	chr1:46767230-46768465	K562	blood:	n/a	chr1:46767482-46767492 chr1:46767893-46767902 chr1:46767737-46767746
29	POLR2A	chr1:46767040-46769691	GM19193	blood:	n/a	n/a
30	CCNT2	chr1:46767188-46769864	K562	blood:	n/a	chr1:46768194-46768203
31	POLR2A	chr1:46767245-46768413	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr1:46766242-46770059	GM12878	blood:	n/a	n/a
33	ZBTB7A	chr1:46767327-46769165	ECC-1	luminal epithelium:	n/a	chr1:46767848-46767856 chr1:46768015-46768023 chr1:46767894-46767903
34	YY1	chr1:46768269-46769672	K562	blood:	n/a	chr1:46769033-46769043 chr1:46769033-46769055 chr1:46769036-46769044 chr1:46769034-46769042
35	POLR2A	chr1:46766997-46769719	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:46766980-46769850	IMR90	lung:	n/a	n/a
37	ELF1	chr1:46767626-46769613	GM12878	blood:	n/a	chr1:46768516-46768528
38	SIN3AK20	chr1:46767438-46769674	PANC-1	pancreas:	n/a	n/a
39	TAF1	chr1:46768340-46769690	SK-N-SH	brain:	n/a	n/a
40	SIN3AK20	chr1:46767625-46769125	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr1:46765846-46769597	Hela-S3	cervix:	n/a	n/a
42	CHD1	chr1:46766034-46770085	IMR90	lung:	n/a	chr1:46768555-46768565 chr1:46768044-46768054
43	MAZ	chr1:46768308-46769356	HepG2	liver:	n/a	n/a
44	POLR2A	chr1:46767370-46769957	MCF10A-Er-Src	breast:	n/a	n/a
45	YY1	chr1:46767640-46769605	GM12878	blood:	n/a	chr1:46767886-46767895 chr1:46769033-46769043 chr1:46767886-46767900 chr1:46769033-46769055 chr1:46768184-46768193 chr1:46767891-46767905 chr1:46769036-46769044 chr1:46767788-46767802 chr1:46769034-46769042 chr1:46768257-46768266
46	POLR2A	chr1:46767216-46769091	K562	blood:	n/a	n/a
47	POU2F2	chr1:46767378-46768515	GM12878	blood:	n/a	chr1:46767501-46767513
48	YY1	chr1:46768203-46769550	ECC-1	luminal epithelium:	n/a	chr1:46769033-46769043 chr1:46769033-46769055 chr1:46769036-46769044 chr1:46769034-46769042 chr1:46768257-46768266
49	MYC	chr1:46768071-46768644	MCF-7	breast:	n/a	n/a
50	POLR2A	chr1:46768315-46768665	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46150273..46155270-chr1:46767408..46770700,6	K562	blood:
2	chr1:46151204..46153647-chr1:46767504..46769158,2	K562	blood:
3	chr1:46763061..46775715-chr1:46803221..46815018,50	K562	blood:
4	chr1:46763061..46775205-chr1:46803159..46817121,53	K562	blood:
5	chr1:45195102..45197641-chr1:46767330..46769394,3	K562	blood:
6	chr1:46047808..46051262-chr1:46767344..46769900,3	K562	blood:
7	chr1:46686929..46689483-chr1:46766855..46768498,2	K562	blood:
8	chr1:46648153..46649948-chr1:46767534..46769281,2	MCF-7	breast:
9	chr1:46768190..46770861-chr1:46804850..46807772,3	MCF-7	breast:
10	chr1:46596666..46599509-chr1:46766938..46769166,2	K562	blood:
11	chr1:46767572..46770121-chr1:46805104..46807027,2	MCF-7	breast:
12	chr1:46724735..46727744-chr1:46766521..46769175,3	K562	blood:
13	chr1:46736743..46741022-chr1:46765806..46768796,4	K562	blood:
14	chr1:46712588..46714730-chr1:46768220..46769843,2	MCF-7	breast:
15	chr1:46595820..46599539-chr1:46766607..46769915,4	K562	blood:
16	chr1:46767029..46769765-chr1:46770513..46776253,5	MCF-7	breast:
17	chr1:46761317..46766795-chr1:46767207..46772068,9	MCF-7	breast:
18	chr1:46709913..46716888-chr1:46765661..46771031,16	K562	blood:
19	chr1:46711557..46715191-chr1:46765613..46771974,14	K562	blood:

Variant related genes	Relation type
UQCRH	TF binding region
LRRC41	TF binding region
ENSG00000132780	Chromatin interaction
ENSG00000117472	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000173660	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000117481	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000132128	Chromatin interaction
ENSG00000085999	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10489770	0.82[MEX][hapmap]
rs10789488	0.82[CHB][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes]
rs10890386	0.82[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes]
rs10890387	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10890388	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10890389	0.87[EUR][1000 genomes]
rs11584233	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12028248	0.81[CEU][hapmap];1.00[MEX][hapmap]
rs12039667	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12044708	0.81[AMR][1000 genomes]
rs12125573	0.92[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12126187	1.00[MEX][hapmap]
rs12141269	1.00[MEX][hapmap]
rs12141928	0.94[MEX][hapmap];0.82[MKK][hapmap]
rs1571138	0.81[ASW][hapmap]
rs17102087	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs2093044	0.83[ASN][1000 genomes]
rs2145408	0.86[ASW][hapmap]
rs324418	0.81[ASW][hapmap]
rs324420	0.86[ASW][hapmap]
rs4660918	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4660919	0.82[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4660920	0.82[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4660921	0.82[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6429596	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6689182	0.82[CHB][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs6692775	0.81[CEU][hapmap]
rs6696085	0.80[CEU][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap]
rs7527133	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs953070	0.81[CEU][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh 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	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1547180	MMACHC	cis	cerebellum	SCAN
rs1547180	SNORD55	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46766400-46772400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:46766600-46770400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:46766600-46773000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:46766800-46770400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:46766800-46770600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:46766800-46770600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:46766800-46771800	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr1:46767000-46768800	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr1:46767000-46769400	Active TSS	HepG2	liver
10	chr1:46767000-46770400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:46767000-46770400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr1:46767000-46770400	Active TSS	Muscle Satellite Cultured Cells	--
13	chr1:46767000-46770400	Active TSS	Ovary	ovary
14	chr1:46767000-46770400	Active TSS	HSMMtube	muscle
15	chr1:46767000-46770600	Active TSS	Fetal Kidney	kidney
16	chr1:46767000-46770600	Active TSS	NHDF-Ad	bronchial
17	chr1:46767000-46770800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr1:46767000-46771000	Active TSS	A549	lung
19	chr1:46767000-46771000	Active TSS	HSMM	muscle
20	chr1:46767000-46771200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr1:46767200-46768600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr1:46767200-46770000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:46767200-46770200	Active TSS	Aorta	Aorta
24	chr1:46767200-46770200	Active TSS	Colon Smooth Muscle	Colon
25	chr1:46767200-46770200	Active TSS	Gastric	stomach
26	chr1:46767200-46770200	Active TSS	Psoas Muscle	Psoas
27	chr1:46767200-46770400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:46767200-46770400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:46767200-46770400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:46767200-46770400	Active TSS	Esophagus	oesophagus
31	chr1:46767200-46770400	Active TSS	Fetal Intestine Large	intestine
32	chr1:46767200-46770400	Active TSS	Small Intestine	intestine
33	chr1:46767200-46770400	Active TSS	HMEC	breast
34	chr1:46767200-46770600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:46767200-46771000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:46767200-46771200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:46767200-46771200	Active TSS	Right Atrium	heart
38	chr1:46767200-46771800	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr1:46767200-46772000	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr1:46767400-46769200	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr1:46767400-46769400	Active TSS	Primary T cells from cord blood	blood
42	chr1:46767400-46769800	Active TSS	Liver	Liver
43	chr1:46767400-46770000	Active TSS	Fetal Muscle Trunk	muscle
44	chr1:46767400-46770000	Active TSS	Placenta	Placenta
45	chr1:46767400-46770000	Active TSS	Placenta Amnion	Placenta Amnion
46	chr1:46767400-46770200	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr1:46767400-46770200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:46767400-46770200	Active TSS	Brain Hippocampus Middle	brain
49	chr1:46767400-46770200	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr1:46767400-46770200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links