Variant report

Variant	rs2246345
Chromosome Location	chr6:1670717-1670718
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1641612..1643839-chr6:1669976..1671799,2	MCF-7	breast:
2	chr6:1670342..1674168-chr6:1677426..1680417,3	MCF-7	breast:
3	chr6:1639221..1644063-chr6:1670120..1672806,4	MCF-7	breast:
4	chr6:1608729..1613027-chr6:1665615..1670900,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11242714	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12197376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210324	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1962433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2317964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2569831	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2569832	0.82[JPT][hapmap]
rs2569842	0.95[JPT][hapmap]
rs2569844	0.82[JPT][hapmap]
rs2569846	0.95[JPT][hapmap]
rs2569849	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2569879	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs2745564	0.82[JPT][hapmap]
rs2814806	0.82[JPT][hapmap]
rs2814807	0.82[JPT][hapmap]
rs2814808	0.82[JPT][hapmap]
rs2814809	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2814812	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2814813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2814816	0.86[JPT][hapmap]
rs2814820	0.95[JPT][hapmap]
rs2814827	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28539691	0.90[ASN][1000 genomes]
rs4060649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4552776	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959586	0.82[JPT][hapmap]
rs62388274	0.90[ASN][1000 genomes]
rs62388275	0.90[ASN][1000 genomes]
rs62388276	0.90[ASN][1000 genomes]
rs62388277	0.90[ASN][1000 genomes]
rs6905377	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6913380	0.88[ASN][1000 genomes]
rs6913557	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6913747	0.88[ASN][1000 genomes]
rs6916770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6917693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6929974	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6930063	0.88[ASN][1000 genomes]
rs6930694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7755553	0.81[JPT][hapmap]
rs7757590	0.82[JPT][hapmap]
rs9328063	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9378302	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9378303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9378304	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9378643	0.95[JPT][hapmap]
rs9378646	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9378647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9378648	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9378649	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9392319	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9392322	0.81[JPT][hapmap]
rs9405144	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9405502	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9501750	0.82[JPT][hapmap]
rs9501751	0.82[JPT][hapmap]
rs9503001	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9503002	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9647654	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1034039	chr6:1427061-1691837	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv538088	chr6:1427061-1691837	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
7	nsv1027393	chr6:1446300-1692019	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv538089	chr6:1446300-1692019	Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv1016594	chr6:1590030-1702529	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
11	nsv530888	chr6:1605768-1739933	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv1015682	chr6:1661111-1717786	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv538092	chr6:1661111-1717786	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2246345	FOXC1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1633000-1679800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:1643800-1671200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:1651600-1679200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:1651800-1678400	Weak transcription	Aorta	Aorta
5	chr6:1653400-1671200	Weak transcription	Esophagus	oesophagus
6	chr6:1662400-1671000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:1662600-1671200	Weak transcription	Gastric	stomach
8	chr6:1667000-1671800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:1667400-1671000	Weak transcription	HepG2	liver
10	chr6:1667800-1687800	Weak transcription	Fetal Intestine Small	intestine
11	chr6:1668000-1671000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:1668200-1671000	Weak transcription	Osteobl	bone
13	chr6:1669800-1673400	Enhancers	Placenta	Placenta
14	chr6:1670200-1670800	Enhancers	GM12878-XiMat	blood
15	chr6:1670200-1671800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:1670200-1671800	Enhancers	HMEC	breast
17	chr6:1670400-1671000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:1670400-1671000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:1670400-1671800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:1670400-1671800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:1670400-1673200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:1670600-1670800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:1670600-1671000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:1670600-1671400	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:1670600-1671600	Enhancers	Hela-S3	cervix

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