Variant report

Variant	rs708118
Chromosome Location	chr1:228201801-228201802
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228200861..228203329-chr1:228205656..228207214,2	MCF-7	breast:
2	chr1:228193376..228197148-chr1:228201050..228204758,3	K562	blood:
3	chr1:228193016..228195089-chr1:228200494..228203250,2	K562	blood:
4	chr1:228199664..228202936-chr1:228261979..228265639,3	MCF-7	breast:
5	chr1:228201206..228204179-chr1:228209528..228212041,2	MCF-7	breast:
6	chr1:228194409..228196147-chr1:228198747..228201814,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154342	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10442629	0.90[EUR][1000 genomes]
rs1636195	1.00[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs1636196	0.96[EUR][1000 genomes]
rs1745413	1.00[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1745416	0.82[AFR][1000 genomes]
rs1745417	0.82[AFR][1000 genomes]
rs1774757	0.92[EUR][1000 genomes]
rs2796055	0.81[CEU][hapmap]
rs3094910	0.83[EUR][1000 genomes]
rs3094911	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3094912	0.81[AFR][1000 genomes]
rs3121309	0.89[CHB][hapmap]
rs3121310	0.89[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs587000	0.81[CEU][hapmap]
rs680148	0.81[CEU][hapmap]
rs697761	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs697762	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs697763	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs708108	0.84[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs708109	1.00[CEU][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes]
rs708110	0.95[EUR][1000 genomes]
rs708113	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs708114	0.81[ASW][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs708115	0.87[AFR][1000 genomes]
rs708116	0.87[AFR][1000 genomes]
rs708117	0.82[AFR][1000 genomes]
rs708121	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs708123	1.00[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs708124	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs7512209	0.82[YRI][hapmap]
rs849900	0.81[CEU][hapmap]
rs964941	0.82[ASW][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv947387	chr1:228140028-228206630	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
10	nsv945349	chr1:228186556-228245135	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs708118	WDR26	cis	cerebellum	SCAN
rs708118	GUK1	cis	parietal	SCAN
rs708118	TMEM63A	cis	cerebellum	SCAN
rs708118	OBSCN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228195200-228213200	Weak transcription	Right Atrium	heart
2	chr1:228199800-228202400	Enhancers	Placenta	Placenta
3	chr1:228200000-228203200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:228200600-228203200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:228200600-228203800	Enhancers	HMEC	breast
6	chr1:228200800-228202600	Enhancers	Esophagus	oesophagus
7	chr1:228201000-228202600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:228201000-228203600	Enhancers	HSMM	muscle
9	chr1:228201200-228202400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
10	chr1:228201200-228202400	Enhancers	HSMMtube	muscle
11	chr1:228201400-228203000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr1:228201600-228202200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:228201600-228203400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:228201800-228202400	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links