Variant report

Variant	rs13948
Chromosome Location	chr1:45480829-45480830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:45480760-45480910	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:45477475-45482921	K562	blood:	n/a	n/a
3	CTCF	chr1:45479767-45480845	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr1:45479883-45480877	HCT-116	colon:	n/a	n/a
5	POLR2A	chr1:45480010-45482910	K562	blood:	n/a	n/a
6	CTCF	chr1:45480049-45480893	K562	blood:	n/a	n/a
7	CTCF	chr1:45480720-45480870	HEEpiC	esophagus:	n/a	n/a
8	RAD21	chr1:45479569-45481167	SK-N-SH	brain:	n/a	n/a
9	CTCF	chr1:45479938-45480921	A549	lung:	n/a	n/a
10	POLR2A	chr1:45480745-45480943	HepG2	liver:	n/a	n/a
11	PML	chr1:45479742-45482654	K562	blood:	n/a	n/a
12	JUN	chr1:45476061-45480910	K562	blood:	n/a	chr1:45477407-45477414 chr1:45477406-45477414 chr1:45477191-45477203
13	POLR2A	chr1:45477763-45483536	K562	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45305082..45310090-chr1:45475264..45482808,8	K562	blood:
2	chr1:45239135..45244789-chr1:45475459..45482236,15	K562	blood:
3	chr1:45476357..45485239-chr1:45761850..45773601,48	K562	blood:
4	chr1:45306981..45310503-chr1:45474976..45481200,7	K562	blood:
5	chr1:45282320..45290015-chr1:45470338..45482903,45	K562	blood:
6	chr1:45194719..45198675-chr1:45474706..45481379,10	K562	blood:
7	chr1:45480602..45482201-chr1:45803688..45807288,4	K562	blood:
8	chr1:45478715..45481443-chr1:45824353..45825976,2	MCF-7	breast:
9	chr1:45281186..45291350-chr1:45463934..45483092,44	K562	blood:
10	chr1:45480075..45485962-chr1:45670647..45674355,5	MCF-7	breast:
11	chr1:45205081..45206794-chr1:45478593..45481166,2	K562	blood:
12	chr1:45265885..45267445-chr1:45480826..45483713,2	K562	blood:
13	chr1:45264355..45267553-chr1:45476139..45481796,8	K562	blood:
14	chr1:45476853..45482658-chr1:45802506..45807966,11	K562	blood:
15	chr1:45264684..45267553-chr1:45478723..45482931,4	MCF-7	breast:
16	chr1:45478895..45481686-chr1:45791437..45793067,2	MCF-7	breast:
17	chr1:45476265..45486633-chr1:45761064..45774272,63	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BTBD19-3	chr1:45480612-45481077	NONHSAT002917

No data

Variant related genes	Relation type
HECTD3	TF binding region
ENSG00000202444	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000238945	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000226499	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000186603	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000117425	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10465876	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749854	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211059	0.89[AFR][1000 genomes]
rs11211066	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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211067	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11556200	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap]
rs11576875	0.94[AFR][1000 genomes]
rs11586398	0.84[AFR][1000 genomes]
rs11588468	0.86[AFR][1000 genomes]
rs11801218	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802780	0.91[AFR][1000 genomes]
rs11806079	0.91[AFR][1000 genomes]
rs11809982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811656	0.86[AFR][1000 genomes]
rs12117191	0.86[AFR][1000 genomes]
rs12117432	0.89[AFR][1000 genomes]
rs12118189	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12125367	0.89[ASW][hapmap];0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12126314	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs12126318	0.84[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap]
rs12127012	0.94[AFR][1000 genomes]
rs12127100	0.86[AFR][1000 genomes]
rs12127262	0.86[AFR][1000 genomes]
rs12134146	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12139143	0.85[CHD][hapmap]
rs12142302	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12143560	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12144152	0.86[AFR][1000 genomes]
rs12239165	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724597	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12724852	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12725055	0.86[AFR][1000 genomes]
rs12731245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12732402	0.94[AFR][1000 genomes]
rs12735549	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12735637	0.89[ASW][hapmap];0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12738542	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs12739545	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12740561	0.89[AFR][1000 genomes]
rs12742371	0.86[AFR][1000 genomes]
rs12749130	0.89[ASW][hapmap];0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12749939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755554	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12755751	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758547	0.91[AFR][1000 genomes]
rs12760109	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17393404	0.91[AFR][1000 genomes]
rs183809	0.84[CEU][hapmap]
rs2050869	0.95[CEU][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2133503	0.86[AFR][1000 genomes]
rs2236576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275598	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2275599	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298005	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263989	0.84[CEU][hapmap];0.89[CHD][hapmap]
rs263991	0.84[CEU][hapmap]
rs263992	0.84[CEU][hapmap]
rs264022	0.84[CEU][hapmap];0.89[CHD][hapmap]
rs264025	0.84[CEU][hapmap];0.89[CHD][hapmap]
rs364482	0.89[CHD][hapmap]
rs3806405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4399199	0.84[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap]
rs56875328	0.94[AFR][1000 genomes]
rs6666806	0.90[GIH][hapmap]
rs6671633	0.82[GIH][hapmap]
rs6678726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6678762	0.94[AFR][1000 genomes]
rs6692713	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs6703452	0.85[CHD][hapmap]
rs68175913	0.83[AFR][1000 genomes]
rs7514998	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7517439	0.85[CHD][hapmap]
rs7519454	0.89[AFR][1000 genomes]
rs7521339	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7525733	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7535347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7541207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553658	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs8681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs998418	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs13948	SNORD55	cis	cerebellum	SCAN
rs13948	UROD	cis	Artery Tibial	GTEx
rs13948	TMEM69	cis	cerebellum	SCAN
rs13948	EIF2B3	cis	cerebellum	SCAN
rs13948	UROD	cis	Thyroid	GTEx
rs13948	SNORD55	cis	parietal	SCAN
rs13948	UROD	cis	Adipose Subcutaneous	GTEx
rs13948	UROD	cis	Nerve Tibial	GTEx
rs13948	UROD	cis	Esophagus Muscularis	GTEx
rs13948	EIF2B3	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45478400-45483200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:45478600-45482600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:45478600-45500000	Weak transcription	Aorta	Aorta
4	chr1:45478800-45481400	Transcr. at gene 5' and 3'	K562	blood
5	chr1:45478800-45482200	Weak transcription	Psoas Muscle	Psoas
6	chr1:45478800-45482600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:45478800-45484000	Weak transcription	Right Atrium	heart
8	chr1:45479000-45482800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:45479000-45483400	Weak transcription	Primary B cells from cord blood	blood
10	chr1:45479000-45484200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:45479000-45484200	Weak transcription	Esophagus	oesophagus
12	chr1:45479000-45485200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:45479000-45493000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:45479200-45481200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:45479200-45482000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:45479200-45484200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:45479400-45481000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
18	chr1:45479400-45481200	Strong transcription	Thymus	Thymus
19	chr1:45479400-45481600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:45479400-45481600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:45479400-45481600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr1:45479400-45481600	Strong transcription	NHEK	skin
23	chr1:45479400-45482000	Strong transcription	Fetal Lung	lung
24	chr1:45479400-45484200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:45479600-45481200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:45479600-45481200	Strong transcription	Colonic Mucosa	Colon
27	chr1:45479600-45481400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:45479600-45481400	Strong transcription	NHLF	lung
29	chr1:45479600-45481600	Strong transcription	Placenta	Placenta
30	chr1:45479600-45481600	Strong transcription	Fetal Stomach	stomach
31	chr1:45479600-45481800	Strong transcription	Primary T cells from cord blood	blood
32	chr1:45479600-45481800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:45479600-45482400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:45479600-45482400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:45479600-45484000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:45479600-45484200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:45479600-45484400	Weak transcription	Right Ventricle	heart
38	chr1:45479800-45481400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:45479800-45481600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:45479800-45481600	Strong transcription	Spleen	Spleen
41	chr1:45479800-45481800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:45479800-45482000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr1:45479800-45482200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:45479800-45482600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:45480000-45481000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:45480000-45481400	Strong transcription	Fetal Thymus	thymus
47	chr1:45480200-45481200	Strong transcription	Fetal Intestine Small	intestine
48	chr1:45480200-45481400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:45480400-45481000	Flanking Active TSS	Fetal Brain Female	brain
50	chr1:45480400-45481400	Strong transcription	Fetal Kidney	kidney

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