Variant report

Variant	rs4602206
Chromosome Location	chr2:38995964-38995965
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	POLR2A	chr2:38995949-38995980	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38991194..38992863-chr2:38993787..38996027,2	MCF-7	breast:
2	chr2:38976319..38979796-chr2:38988969..38996616,16	MCF-7	breast:
3	chr2:38973912..38980240-chr2:38989822..38999883,17	MCF-7	breast:
4	chr2:38977122..38981176-chr2:38994666..38999219,6	K562	blood:

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

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10173118	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10173240	0.89[CEU][hapmap];0.94[CHB][hapmap];0.81[EUR][1000 genomes]
rs10176932	0.94[CHB][hapmap]
rs10197412	0.96[CEU][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865143	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10865144	0.81[EUR][1000 genomes]
rs11124646	0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1138974	0.83[ASN][1000 genomes]
rs11694383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11889280	0.80[ASN][1000 genomes]
rs12465043	0.80[EUR][1000 genomes]
rs12469681	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12472454	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12473036	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12477252	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12618118	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12712621	0.88[CHB][hapmap]
rs12991609	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12996194	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13011311	0.84[ASN][1000 genomes]
rs13011522	0.86[EUR][1000 genomes]
rs13014136	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13029406	0.88[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13383541	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs13411868	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13417196	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1529625	0.88[CEU][hapmap]
rs1530852	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1530853	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1979142	0.89[CEU][hapmap];0.94[CHB][hapmap];0.81[EUR][1000 genomes]
rs1997377	0.88[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2037875	0.96[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2272445	0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2373473	0.90[JPT][hapmap]
rs3099940	0.90[JPT][hapmap]
rs3099941	0.90[JPT][hapmap]
rs3099943	1.00[JPT][hapmap]
rs3099945	1.00[JPT][hapmap]
rs3099952	0.89[ASN][1000 genomes]
rs3099956	0.89[JPT][hapmap]
rs3099958	0.89[JPT][hapmap]
rs3099960	0.86[ASN][1000 genomes]
rs3099965	0.87[EUR][1000 genomes]
rs3112140	0.81[EUR][1000 genomes]
rs3112198	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3112200	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3112205	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3112209	0.81[ASN][1000 genomes]
rs3112210	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112215	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs3112216	0.80[ASN][1000 genomes]
rs3770681	0.94[CHB][hapmap]
rs4630748	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670268	0.86[JPT][hapmap]
rs4670891	0.86[ASN][1000 genomes]
rs4670894	0.82[ASN][1000 genomes]
rs4670897	0.81[EUR][1000 genomes]
rs56393601	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62144837	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6544175	0.84[ASN][1000 genomes]
rs6715866	1.00[CEU][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6728394	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6731386	0.84[ASN][1000 genomes]
rs6736004	0.82[ASN][1000 genomes]
rs6738069	0.89[JPT][hapmap]
rs6746818	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs6753251	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6756847	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7419616	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7419838	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7581263	0.84[ASN][1000 genomes]
rs7581653	0.84[ASN][1000 genomes]
rs7589162	0.82[CEU][hapmap];0.94[CHB][hapmap]
rs7596239	0.83[ASN][1000 genomes]
rs7603676	0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7603821	0.84[ASN][1000 genomes]
rs8179664	0.89[JPT][hapmap]

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
rs4602206	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 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	chr2:38993400-38998800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:38993600-38999000	Weak transcription	Osteobl	bone
4	chr2:38993800-38997200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:38994200-38998200	Enhancers	Fetal Heart	heart
6	chr2:38994600-38998800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:38994600-39004600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:38995200-38998800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:38995400-38998800	Weak transcription	HepG2	liver
10	chr2:38995600-38999000	Weak transcription	Liver	Liver

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