Variant report

Variant	rs6788750
Chromosome Location	chr3:99774720-99774721
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99626736..99629187-chr3:99773539..99775564,2	MCF-7	breast:
2	chr3:99773385..99774935-chr3:99776387..99778505,2	K562	blood:
3	chr3:99774401..99777236-chr3:99780310..99781935,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11711935	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16841874	0.88[LWK][hapmap];0.94[MKK][hapmap]
rs1718235	0.84[LWK][hapmap];0.94[MKK][hapmap]
rs2449106	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs4244712	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs4928230	0.86[LWK][hapmap];0.94[MKK][hapmap]
rs6805884	0.91[CEU][hapmap]
rs7619512	0.82[AFR][1000 genomes]
rs7650727	0.91[MKK][hapmap]
rs793439	0.86[LWK][hapmap];0.94[MKK][hapmap]
rs793502	0.84[LWK][hapmap];0.94[MKK][hapmap]
rs813218	0.84[LWK][hapmap];0.94[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6788750	C3orf26	cis	multi-tissue	Pritchard
rs6788750	OR5H6	cis	cerebellum	SCAN
rs6788750	SENP7	cis	parietal	SCAN
rs6788750	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99762000-99778200	Weak transcription	Ovary	ovary
3	chr3:99767000-99777000	Weak transcription	Aorta	Aorta
4	chr3:99767400-99775000	Weak transcription	Psoas Muscle	Psoas
5	chr3:99767400-99779600	Weak transcription	Left Ventricle	heart
6	chr3:99767600-99779400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:99767600-99801000	Weak transcription	HSMM	muscle
8	chr3:99767800-99774800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:99767800-99777000	Weak transcription	HMEC	breast
10	chr3:99768200-99780400	Weak transcription	GM12878-XiMat	blood
11	chr3:99768400-99788000	Weak transcription	Primary B cells from cord blood	blood
12	chr3:99769000-99776400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:99770800-99787600	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:99771200-99775000	Enhancers	Fetal Intestine Large	intestine
15	chr3:99771200-99775000	Enhancers	Fetal Intestine Small	intestine
16	chr3:99771600-99778400	Weak transcription	K562	blood
17	chr3:99772200-99776400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:99772400-99777400	Weak transcription	HSMMtube	muscle
19	chr3:99773200-99776200	Weak transcription	Adipose Nuclei	Adipose
20	chr3:99773200-99776600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:99773400-99774800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:99773400-99776600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:99774000-99776200	Weak transcription	HepG2	liver
24	chr3:99774000-99794800	Weak transcription	Stomach Mucosa	stomach
25	chr3:99774200-99775200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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