Variant report

Variant	rs7586110
Chromosome Location	chr2:234590527-234590528
allele	G/T
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	FOS	chr2:234590208-234590532	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr2:234590170-234590529	MCF10A-Er-Src	breast:	n/a	chr2:234590375-234590386 chr2:234590254-234590265
3	FOS	chr2:234590183-234590592	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr2:234590218-234590527	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr2:234590191-234590589	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
UGT1A7	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10167119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs10168155	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10168333	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10168416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10171367	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10173355	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10175809	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10178992	0.88[CEU][hapmap]
rs10179094	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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10180090	0.82[EUR][1000 genomes]
rs10189426	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10197460	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs10202865	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10203266	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10445704	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1105879	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1105880	1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11673726	0.88[CEU][hapmap]
rs11680450	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11692021	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11692664	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11888459	0.88[CEU][hapmap]
rs11891311	0.88[CEU][hapmap]
rs11902131	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12615708	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12623271	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13002774	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13015720	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17863787	0.81[GIH][hapmap]
rs1875263	0.88[CEU][hapmap]
rs1983023	0.96[CEU][hapmap]
rs2018985	0.96[CEU][hapmap]
rs2070959	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2602376	0.81[GIH][hapmap]
rs2741045	0.81[GIH][hapmap]
rs35984508	0.86[ASN][1000 genomes]
rs3806598	0.87[ASN][1000 genomes]
rs4261716	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4338954	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4347832	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4530361	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4553819	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45615240	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6724485	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6725478	0.96[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs6736508	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6736743	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6753320	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6753569	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6759892	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7349250	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7563561	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7564935	0.88[CEU][hapmap]
rs7571915	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7577677	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]
rs7583278	0.96[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap]
rs7592281	0.86[ASN][1000 genomes]
rs7604115	0.88[CEU][hapmap]
rs7608175	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs869283	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv3340677	chr2:234580879-234591324	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv979185	chr2:234590426-234591548	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
7	nsv876016	chr2:234590527-234601669	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7586110	EFHD1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234559800-234592800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr2:234588000-234593000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:234588600-234597000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:234589000-234590800	Enhancers	Liver	Liver
5	chr2:234589400-234590600	Weak transcription	Esophagus	oesophagus
6	chr2:234589400-234590800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:234589800-234593000	Weak transcription	A549	lung
8	chr2:234590000-234597800	Weak transcription	Colonic Mucosa	Colon
9	chr2:234590200-234591800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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