Variant report

Variant	rs514235
Chromosome Location	chr1:93438456-93438457
allele	A/G
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	GTF2F1	chr1:93438419-93438498	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr1:93438376-93438574	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr1:93438333-93438708	H1-hESC	embryonic stem cell:	n/a	n/a
4	CEBPB	chr1:93438184-93438514	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr1:93438332-93438601	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:93438373-93438614	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:93438265-93438670	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93428670..93431519-chr1:93436663..93439033,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-970P	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1011663	0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs10747454	0.88[ASN][1000 genomes]
rs10874752	0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11164827	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs11164838	0.88[CHB][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap]
rs11164848	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11164849	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11164850	0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11164851	0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11164854	0.87[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs12049007	0.81[ASN][1000 genomes]
rs12092304	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12120036	0.81[ASN][1000 genomes]
rs12130044	0.87[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs12133990	0.85[ASN][1000 genomes]
rs12144226	0.85[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs12747275	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1678784	0.86[ASN][1000 genomes]
rs2086314	0.81[ASN][1000 genomes]
rs2127398	0.81[ASN][1000 genomes]
rs2127400	0.81[ASN][1000 genomes]
rs28561471	0.88[ASN][1000 genomes]
rs3943283	0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4515797	0.90[ASN][1000 genomes]
rs4847226	0.80[ASN][1000 genomes]
rs4847386	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4847389	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs521428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs534409	0.90[ASN][1000 genomes]
rs567613	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs594527	0.88[ASN][1000 genomes]
rs606344	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs619784	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs641462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs660870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs663112	0.83[ASN][1000 genomes]
rs6671078	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681240	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6681345	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6681429	0.81[ASN][1000 genomes]
rs7517539	0.81[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs7524934	0.87[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs753391	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs770883	0.87[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs770884	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs945630	0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs514235	MTF2	cis	Skin Sun Exposed Lower leg	GTEx
rs514235	FAM69A	cis	Artery Tibial	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93428400-93445800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:93431600-93438600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:93431600-93438600	Weak transcription	Thymus	Thymus
4	chr1:93433200-93445000	Enhancers	Primary B cells from cord blood	blood
5	chr1:93433600-93439200	Enhancers	Fetal Heart	heart
6	chr1:93434000-93439400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:93434200-93445600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:93435400-93440600	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:93435800-93438600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:93436200-93441800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:93436600-93440600	Weak transcription	Pancreas	Pancrea
12	chr1:93437000-93441800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr1:93437600-93438600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:93437600-93438600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr1:93437600-93439600	Enhancers	Dnd41	blood
16	chr1:93437600-93441400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr1:93437800-93438600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:93437800-93439000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:93437800-93439000	Enhancers	Aorta	Aorta
20	chr1:93437800-93439600	Enhancers	Primary hematopoietic stem cells	blood
21	chr1:93437800-93439600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:93437800-93439600	Enhancers	K562	blood
23	chr1:93437800-93439600	Enhancers	NHEK	skin
24	chr1:93437800-93439800	Enhancers	Primary T cells from cord blood	blood
25	chr1:93438000-93438600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:93438000-93438800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:93438000-93438800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:93438000-93439400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:93438000-93439600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr1:93438000-93439600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr1:93438000-93439600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr1:93438000-93439600	Flanking Active TSS	GM12878-XiMat	blood
33	chr1:93438000-93439600	Enhancers	HMEC	breast
34	chr1:93438000-93441800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:93438000-93443600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:93438200-93438600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
37	chr1:93438200-93438600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:93438200-93438600	Enhancers	Adipose Nuclei	Adipose
39	chr1:93438200-93438600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr1:93438200-93438600	Enhancers	Colonic Mucosa	Colon
41	chr1:93438200-93438600	Bivalent Enhancer	Fetal Muscle Leg	muscle
42	chr1:93438200-93438600	Enhancers	Placenta	Placenta
43	chr1:93438200-93438600	Enhancers	Right Ventricle	heart
44	chr1:93438200-93438600	Enhancers	Spleen	Spleen
45	chr1:93438200-93438800	Enhancers	H1 Cell Line	embryonic stem cell
46	chr1:93438200-93438800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
47	chr1:93438200-93438800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
48	chr1:93438200-93438800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
49	chr1:93438200-93438800	Enhancers	Esophagus	oesophagus
50	chr1:93438200-93438800	Enhancers	Left Ventricle	heart

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