Variant report

Variant	rs12618118
Chromosome Location	chr2:38994418-38994419
allele	C/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	TCF7L2	chr2:38994039-38994436	MCF-7	breast:	n/a	chr2:38994200-38994214
2	FOXA1	chr2:38994305-38994733	HepG2	liver:	n/a	chr2:38994575-38994587
3	FOXA1	chr2:38994295-38994716	HepG2	liver:	n/a	chr2:38994575-38994587
4	FOXA2	chr2:38994381-38994630	HepG2	liver:	n/a	chr2:38994575-38994587
5	FOXA1	chr2:38994291-38994832	HepG2	liver:	n/a	chr2:38994575-38994587

No.	Distal block	Cell Line	Cell type
1	chr2:38992665..38995431-chr2:39003330..39006208,3	K562	blood:
2	chr2:38974221..38979921-chr2:38986851..38994572,21	K562	blood:
3	chr2:38992046..38994768-chr2:39003878..39006153,3	MCF-7	breast:
4	chr2:38993209..38995928-chr2:39007575..39009225,2	MCF-7	breast:
5	chr2:38989424..38992394-chr2:38992856..38995438,2	K562	blood:
6	chr2:38991194..38992863-chr2:38993787..38996027,2	MCF-7	breast:
7	chr2:38976319..38979796-chr2:38988969..38996616,16	MCF-7	breast:
8	chr2:38973912..38980240-chr2:38989822..38999883,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232114	TF binding region
ENSG00000152147	Chromatin interaction
ENSG00000227238	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10173118	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10173240	0.82[EUR][1000 genomes]
rs10197412	0.91[CHB][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865143	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10865144	0.82[EUR][1000 genomes]
rs1138975	0.86[ASN][1000 genomes]
rs11694383	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11898812	1.00[CHB][hapmap]
rs12465043	0.81[EUR][1000 genomes]
rs12469681	0.89[EUR][1000 genomes]
rs12472454	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12473036	0.89[EUR][1000 genomes]
rs12474770	0.83[ASN][1000 genomes]
rs12477252	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12621103	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs12991609	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12996194	0.83[EUR][1000 genomes]
rs13011522	0.88[EUR][1000 genomes]
rs13014136	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13024811	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs13029406	0.84[EUR][1000 genomes]
rs13383541	0.83[EUR][1000 genomes]
rs13411868	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13417196	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1529625	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs1530852	0.88[EUR][1000 genomes]
rs1530853	0.88[EUR][1000 genomes]
rs1979142	0.82[EUR][1000 genomes]
rs1979143	0.90[CHB][hapmap]
rs2037875	0.91[CHB][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3097713	0.91[CHB][hapmap]
rs3099961	0.86[ASN][1000 genomes]
rs3099965	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3099968	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs3099971	0.89[ASN][1000 genomes]
rs3099990	0.83[CHB][hapmap]
rs3112140	0.82[EUR][1000 genomes]
rs3112142	0.81[CHB][hapmap]
rs3112178	0.90[CHB][hapmap]
rs3112183	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs3112184	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3112186	0.89[ASN][1000 genomes]
rs3112188	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3112189	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3112191	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3112192	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3112194	0.85[ASN][1000 genomes]
rs3112196	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs3112198	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3112200	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3112204	0.86[ASN][1000 genomes]
rs3112205	0.88[EUR][1000 genomes]
rs3112210	0.88[EUR][1000 genomes]
rs3112216	0.80[EUR][1000 genomes]
rs3134628	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs3134629	0.85[ASN][1000 genomes]
rs3134630	0.85[ASN][1000 genomes]
rs3134637	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs35387882	0.89[ASN][1000 genomes]
rs3731838	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs4602206	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4630748	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4670891	0.80[AFR][1000 genomes]
rs4670892	0.83[ASN][1000 genomes]
rs4670897	0.82[EUR][1000 genomes]
rs56393601	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62144837	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6715866	0.91[CHB][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6717670	1.00[CHB][hapmap]
rs6746818	0.92[CHB][hapmap];0.80[YRI][hapmap];0.90[ASN][1000 genomes]
rs6753251	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7419616	0.88[EUR][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
4	nsv1014616	chr2:38985472-39022893	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12618118	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:38992200-38995200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:38993200-38994600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:38993200-38994600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:38993400-38998800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:38993600-38999000	Weak transcription	Osteobl	bone
7	chr2:38993800-38997200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:38994200-38994600	Enhancers	HMEC	breast
9	chr2:38994200-38995400	Enhancers	HepG2	liver
10	chr2:38994200-38995600	Enhancers	Liver	Liver
11	chr2:38994200-38998200	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links