Variant report

Variant	rs3758655
Chromosome Location	chr11:47703943-47703944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47702332..47704509-chr11:47712324..47714813,2	K562	blood:
2	chr11:47702117..47703985-chr11:47709278..47711323,2	MCF-7	breast:
3	chr11:47701464..47704158-chr11:47707754..47709950,3	K562	blood:
4	chr11:47662359..47664055-chr11:47702569..47704860,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109919	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10458915	0.87[ASN][1000 genomes]
rs1056387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10742814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs10742817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10742820	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10742824	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10769285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769288	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs10769299	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10769300	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10838726	0.89[JPT][hapmap]
rs10838732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs10838736	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838739	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838745	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838751	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838758	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838759	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838760	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838763	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10838766	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838767	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838768	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838769	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838771	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838773	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838774	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10838775	0.87[ASN][1000 genomes]
rs10838776	0.87[ASN][1000 genomes]
rs10838777	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10838782	0.83[ASN][1000 genomes]
rs10838784	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11039329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039332	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11039336	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039354	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039373	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039376	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039377	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039379	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039392	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039401	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039402	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039414	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039415	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039419	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039429	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039431	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039432	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12225854	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12226431	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12226590	0.81[AMR][1000 genomes]
rs12285933	1.00[YRI][hapmap]
rs12286721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12360643	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12362318	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12365079	0.85[ASN][1000 genomes]
rs12366244	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12421563	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12576933	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12785949	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1563820	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1563821	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2125838	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2170815	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2203712	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2290851	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28617307	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2869534	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2869541	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2904127	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3740699	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap]
rs3816605	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3886262	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4539273	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4543938	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752792	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752796	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752798	0.83[ASN][1000 genomes]
rs4752858	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752865	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60833259	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61895760	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6485758	0.89[JPT][hapmap]
rs6485763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6485773	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6485775	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6485778	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6485786	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7101597	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7102205	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7105791	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7107792	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7107922	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7108479	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7110300	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7111509	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7111576	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111606	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7112248	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7114011	0.94[JPT][hapmap]
rs7114813	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7115228	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7116320	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7116346	0.83[ASN][1000 genomes]
rs7116970	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7118747	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7120548	0.89[JPT][hapmap]
rs7122182	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7122217	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7123952	0.87[ASN][1000 genomes]
rs7124396	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7126378	0.80[AMR][1000 genomes]
rs7129237	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7129797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7131262	0.94[JPT][hapmap]
rs754434	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7925211	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7927445	0.94[JPT][hapmap]
rs7929014	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7929725	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7932703	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7933019	0.89[JPT][hapmap]
rs7933184	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7933896	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7935344	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7935521	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935528	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7936948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939420	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941399	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7943213	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943464	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7945312	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7948468	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7950674	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs9633830	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3758655	C1QTNF4	cis	multi-tissue	Pritchard
rs3758655	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs3758655	FNBP4	cis	lesional skin	skin_eQTL
rs3758655		cis	Lymphoblastoid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47689400-47711200	Weak transcription	Liver	Liver
2	chr11:47703200-47704200	Enhancers	Rectal Mucosa Donor 29	rectum
3	chr11:47703200-47704400	Enhancers	K562	blood
4	chr11:47703200-47704600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:47703200-47704600	Enhancers	Fetal Lung	lung
6	chr11:47703400-47704200	Enhancers	HepG2	liver
7	chr11:47703400-47704400	Enhancers	Duodenum Mucosa	Duodenum
8	chr11:47703400-47704400	Enhancers	Fetal Intestine Small	intestine
9	chr11:47703400-47704400	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr11:47703400-47704600	Enhancers	Fetal Intestine Large	intestine
11	chr11:47703600-47704400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr11:47703800-47704400	Enhancers	Hela-S3	cervix

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