Variant report

Variant	rs7144658
Chromosome Location	chr14:38061742-38061743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr14:38060607-38061760	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr14:38060292-38061770	A549	lung:	n/a	n/a
3	E2F6	chr14:38061361-38062020	A549	lung:	n/a	n/a
4	POLR2A	chr14:38060558-38062366	MCF-7	breast:	n/a	n/a
5	PML	chr14:38060516-38062586	MCF-7	breast:	n/a	n/a
6	SIN3AK20	chr14:38060259-38066080	MCF-7	breast:	n/a	n/a
7	MAX	chr14:38060594-38061847	H1-hESC	embryonic stem cell:	n/a	n/a
8	HDAC2	chr14:38060392-38062489	MCF-7	breast:	n/a	n/a
9	PML	chr14:38060460-38062367	MCF-7	breast:	n/a	n/a
10	MAX	chr14:38060450-38061961	A549	lung:	n/a	n/a
11	POLR2A	chr14:38061138-38061932	A549	lung:	n/a	n/a
12	POLR2A	chr14:38060432-38062293	ProgFib	skin:	n/a	n/a
13	GATA3	chr14:38061309-38062292	MCF-7	breast:	n/a	n/a
14	SUZ12	chr14:38061146-38062243	H1-hESC	embryonic stem cell:	n/a	n/a
15	NR2F2	chr14:38060475-38062546	MCF-7	breast:	n/a	n/a
16	YY1	chr14:38061278-38061990	H1-hESC	embryonic stem cell:	n/a	n/a
17	MYC	chr14:38061440-38061743	MCF-7	breast:	n/a	n/a
18	CTBP2	chr14:38060581-38062070	H1-hESC	embryonic stem cell:	n/a	n/a
19	YY1	chr14:38060896-38061980	HepG2	liver:	n/a	n/a
20	POLR2A	chr14:38059290-38065931	MCF-7	breast:	n/a	n/a
21	MAX	chr14:38060376-38062437	MCF-7	breast:	n/a	n/a
22	YY1	chr14:38061336-38061870	H1-hESC	embryonic stem cell:	n/a	n/a
23	TCF12	chr14:38060504-38062183	A549	lung:	n/a	n/a
24	JUND	chr14:38060359-38062588	MCF-7	breast:	n/a	n/a
25	POLR2A	chr14:38060674-38062003	A549	lung:	n/a	n/a
26	POLR2A	chr14:38061144-38062114	MCF-7	breast:	n/a	n/a
27	ELF1	chr14:38060497-38062465	MCF-7	breast:	n/a	chr14:38061946-38061958
28	POLR2A	chr14:38061671-38062421	HepG2	liver:	n/a	n/a
29	POLR2A	chr14:38061223-38062968	HepG2	liver:	n/a	n/a
30	POLR2A	chr14:38061199-38062269	HepG2	liver:	n/a	n/a
31	CTCF	chr14:38061600-38061750	Caco-2	colon:	n/a	n/a
32	POLR2A	chr14:38061533-38061750	A549	lung:	n/a	n/a
33	POLR2A	chr14:38061738-38062390	HepG2	liver:	n/a	n/a
34	HEY1	chr14:38061267-38065955	HepG2	liver:	n/a	chr14:38065572-38065587 chr14:38064280-38064295 chr14:38063965-38063980 chr14:38064069-38064084 chr14:38064057-38064072 chr14:38063797-38063812
35	ZNF263	chr14:38061171-38062146	HEK293-T-REx	kidney:	n/a	n/a
36	MAX	chr14:38061272-38061810	A549	lung:	n/a	n/a
37	FOSL2	chr14:38061682-38061938	A549	lung:	n/a	n/a
38	YY1	chr14:38061284-38061911	A549	lung:	n/a	n/a
39	ZNF143	chr14:38061424-38061743	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:37744550..37746871-chr14:38059550..38062065,2	MCF-7	breast:
2	chr14:38061292..38062805-chr14:38087179..38088948,2	MCF-7	breast:
3	chr14:38061188..38062037-chr14:38183857..38184453,2	MCF-7	breast:
4	chr14:37996620..37999759-chr14:38060620..38062986,3	MCF-7	breast:
5	chr14:37924566..37927073-chr14:38060566..38062784,2	MCF-7	breast:
6	chr14:38003108..38005323-chr14:38059907..38061947,2	MCF-7	breast:
7	chr14:38060623..38062543-chr4:141076075..141078577,2	MCF-7	breast:
8	chr14:38055708..38063394-chr14:38063498..38068319,8	K562	blood:
9	chr14:38061626..38064274-chr8:144362134..144365132,2	MCF-7	breast:
10	chr14:37731472..37733246-chr14:38060600..38063260,2	MCF-7	breast:
11	chr14:38061110..38061929-chr14:38184193..38185061,2	MCF-7	breast:
12	chr14:38060569..38062165-chr14:38339643..38341361,2	MCF-7	breast:
13	chr14:38059647..38062011-chr19:58890686..58893348,2	MCF-7	breast:
14	chr14:38059772..38062294-chr6:35436080..35437583,2	MCF-7	breast:
15	chr14:37977669..37980526-chr14:38060967..38062630,2	MCF-7	breast:
16	chr14:37709149..37730989-chr14:38048141..38067789,135	MCF-7	breast:
17	chr14:38058730..38062004-chr14:38152244..38154718,3	MCF-7	breast:
18	chr14:38060438..38062133-chr14:38130712..38132708,2	MCF-7	breast:
19	chr14:38051890..38052684-chr14:38061075..38061786,2	MCF-7	breast:
20	chr14:38010426..38020494-chr14:38050537..38062032,33	MCF-7	breast:
21	chr14:37708906..37733371-chr14:38048131..38068843,170	MCF-7	breast:
22	chr14:38061358..38063507-chr3:161089489..161091930,2	MCF-7	breast:
23	chr14:37903287..37907312-chr14:38059908..38064571,5	MCF-7	breast:
24	chr14:38061711..38062291-chr14:38118987..38119728,2	MCF-7	breast:

No data

Variant related genes	Relation type
TTC6	TF binding region
ENSG00000129514	Chromatin interaction
ENSG00000151338	Chromatin interaction
ENSG00000198755	Chromatin interaction
ENSG00000152475	Chromatin interaction
ENSG00000253716	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000207046	Chromatin interaction
ENSG00000139865	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1008236	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs10133438	0.86[CHB][hapmap]
rs10143976	0.86[CHD][hapmap]
rs10144334	0.85[ASN][1000 genomes]
rs10145379	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145473	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs10151200	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs10400689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs1057536	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11156961	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs11156962	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1155456	0.86[CHD][hapmap]
rs1158701	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs1159151	0.86[CHB][hapmap]
rs11623989	0.82[CHD][hapmap]
rs11627807	0.97[ASN][1000 genomes]
rs11627844	0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1169873	0.86[CHD][hapmap]
rs11846416	0.85[ASN][1000 genomes]
rs12147939	0.83[CEU][hapmap]
rs12884884	0.82[GIH][hapmap]
rs1547009	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs17768343	0.82[GIH][hapmap];0.81[TSI][hapmap]
rs1814005	0.86[CHD][hapmap]
rs1884798	0.87[ASN][1000 genomes]
rs1884803	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs1950824	0.87[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs1950826	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs1955934	0.82[CHD][hapmap]
rs1956427	0.86[CHD][hapmap]
rs1956429	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1956433	0.86[CHD][hapmap]
rs1956437	0.86[CHD][hapmap]
rs1956442	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1956443	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1980675	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs2006729	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs2146133	0.86[CHD][hapmap]
rs2180609	0.86[CHD][hapmap]
rs2415404	0.86[CHD][hapmap]
rs4900918	0.86[CHD][hapmap]
rs4900945	0.86[CHD][hapmap]
rs4900958	0.80[CEU][hapmap]
rs4900969	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap]
rs4901012	0.92[ASN][1000 genomes]
rs6571814	0.86[CHD][hapmap]
rs7146299	0.86[CHD][hapmap]
rs7146958	0.85[ASN][1000 genomes]
rs7147379	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs7153426	0.86[CHD][hapmap]
rs7153867	0.85[ASN][1000 genomes]
rs7159456	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs7160774	0.92[ASN][1000 genomes]
rs7161228	0.92[CEU][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7161326	0.85[CHD][hapmap]
rs7493775	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs762083	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8005136	0.82[CHD][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap]
rs8016138	0.85[ASN][1000 genomes]
rs8019713	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs9322981	0.83[ASN][1000 genomes]
rs968350	0.83[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs996916	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[ASN][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	nsv530038	chr14:37590543-38336191	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv826923	chr14:38017619-38108645	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv832772	chr14:38030300-38225921	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
4	nsv901642	chr14:38041870-38081005	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv901643	chr14:38047789-38081005	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
6	nsv901644	chr14:38049107-38064738	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv901645	chr14:38051035-38064215	Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv901646	chr14:38051035-38081005	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv901647	chr14:38052110-38064738	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
10	nsv901648	chr14:38052110-38065813	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
11	nsv916985	chr14:38052347-38838551	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
12	nsv901649	chr14:38053334-38065813	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7144658	BRMS1L	cis	cerebellum	SCAN
rs7144658	SEC23A	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38053400-38062800	Weak transcription	Hela-S3	cervix
2	chr14:38056200-38065600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
3	chr14:38056400-38066000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
4	chr14:38057000-38065400	Active TSS	Liver	Liver
5	chr14:38058600-38062200	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr14:38059600-38063200	Bivalent/Poised TSS	Stomach Mucosa	stomach
7	chr14:38059800-38065600	Active TSS	A549	lung
8	chr14:38060000-38063200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
9	chr14:38060200-38062400	Bivalent/Poised TSS	Colonic Mucosa	Colon
10	chr14:38060400-38062200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr14:38060400-38062400	Bivalent/Poised TSS	Small Intestine	intestine
12	chr14:38060400-38064000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
13	chr14:38060600-38061800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr14:38060600-38061800	Bivalent Enhancer	HMEC	breast
15	chr14:38060600-38062000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
16	chr14:38060600-38062000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr14:38060600-38062000	Bivalent Enhancer	Spleen	Spleen
18	chr14:38060600-38062200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr14:38060600-38062200	Transcr. at gene 5' and 3'	Gastric	stomach
20	chr14:38060600-38062400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr14:38060600-38062400	ZNF genes & repeats	Lung	lung
22	chr14:38060600-38064000	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
23	chr14:38060800-38061800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
24	chr14:38060800-38062200	Enhancers	Pancreas	Pancrea
25	chr14:38060800-38062200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
26	chr14:38060800-38062400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr14:38060800-38062400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
28	chr14:38061000-38061800	Bivalent Enhancer	Ovary	ovary
29	chr14:38061000-38061800	Genic enhancers	HepG2	liver
30	chr14:38061000-38062000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr14:38061200-38061800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr14:38061200-38062200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr14:38061400-38061800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr14:38061400-38061800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr14:38061400-38061800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
36	chr14:38061400-38061800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr14:38061400-38062000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr14:38061400-38062000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr14:38061400-38063200	Bivalent/Poised TSS	Fetal Stomach	stomach
40	chr14:38061600-38061800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
41	chr14:38061600-38061800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr14:38061600-38061800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
43	chr14:38061600-38061800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
44	chr14:38061600-38062000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr14:38061600-38062800	Active TSS	Esophagus	oesophagus

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