Variant report

Variant	rs12991609
Chromosome Location	chr2:38989961-38989962
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38974221..38979921-chr2:38986851..38994572,21	K562	blood:
2	chr2:38973025..38976072-chr2:38989424..38992491,3	MCF-7	breast:
3	chr2:38976319..38979796-chr2:38988969..38996616,16	MCF-7	breast:
4	chr2:38973912..38980240-chr2:38989822..38999883,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10173118	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10173240	0.80[EUR][1000 genomes]
rs10197412	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10865143	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10865144	0.81[EUR][1000 genomes]
rs1138975	0.87[ASN][1000 genomes]
rs11694383	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12469681	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12472454	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12473036	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12474770	0.86[ASN][1000 genomes]
rs12477252	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12618118	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12996194	0.82[EUR][1000 genomes]
rs13011522	0.86[EUR][1000 genomes]
rs13014136	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13024811	0.85[ASN][1000 genomes]
rs13029406	0.82[EUR][1000 genomes]
rs13383541	0.81[EUR][1000 genomes]
rs13411868	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13417196	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1530852	0.86[EUR][1000 genomes]
rs1530853	0.86[EUR][1000 genomes]
rs1979142	0.80[EUR][1000 genomes]
rs2037875	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3097713	0.82[ASN][1000 genomes]
rs3099961	0.84[ASN][1000 genomes]
rs3099965	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3099971	0.86[ASN][1000 genomes]
rs3112140	0.81[EUR][1000 genomes]
rs3112183	0.82[ASN][1000 genomes]
rs3112184	0.86[ASN][1000 genomes]
rs3112186	0.86[ASN][1000 genomes]
rs3112188	0.86[ASN][1000 genomes]
rs3112189	0.86[ASN][1000 genomes]
rs3112191	0.86[ASN][1000 genomes]
rs3112192	0.86[ASN][1000 genomes]
rs3112194	0.82[ASN][1000 genomes]
rs3112196	0.84[ASN][1000 genomes]
rs3112198	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3112200	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3112204	0.84[ASN][1000 genomes]
rs3112205	0.86[EUR][1000 genomes]
rs3112210	0.86[EUR][1000 genomes]
rs3134628	0.82[ASN][1000 genomes]
rs3134629	0.82[ASN][1000 genomes]
rs3134630	0.82[ASN][1000 genomes]
rs3134637	0.85[ASN][1000 genomes]
rs35387882	0.92[ASN][1000 genomes]
rs3731838	0.86[ASN][1000 genomes]
rs4602206	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4630748	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4670892	0.86[ASN][1000 genomes]
rs4670897	0.80[EUR][1000 genomes]
rs56393601	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62144837	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6715866	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6746818	0.90[ASN][1000 genomes]
rs6753251	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7419616	0.86[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
rs12991609	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 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	chr2:38989400-38990400	Weak transcription	HepG2	liver

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