Variant report

Variant	rs9392349
Chromosome Location	chr6:1992885-1992886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1992439..1995123-chr6:2017322..2020251,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXC1-11	chr6:1992403-1994306	NONHSAT106575

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11242731	0.82[ASN][1000 genomes]
rs11758621	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12206139	0.84[ASN][1000 genomes]
rs12212324	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13218855	0.90[ASN][1000 genomes]
rs1802	0.85[ASN][1000 genomes]
rs2076916	0.93[ASN][1000 genomes]
rs2875725	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs35546016	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4308609	0.85[ASN][1000 genomes]
rs4959620	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs501038	0.86[ASN][1000 genomes]
rs538391	0.86[ASN][1000 genomes]
rs635234	0.88[ASN][1000 genomes]
rs6596868	0.91[ASN][1000 genomes]
rs668674	0.86[ASN][1000 genomes]
rs6909371	0.90[ASN][1000 genomes]
rs6910252	0.91[ASN][1000 genomes]
rs6922565	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7772545	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328080	0.93[ASN][1000 genomes]
rs9378669	0.96[ASN][1000 genomes]
rs9391942	0.81[AFR][1000 genomes]
rs9392351	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9405537	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9405545	0.87[ASN][1000 genomes]
rs9503076	0.88[ASN][1000 genomes]
rs9503080	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1985000-2010200	Weak transcription	Fetal Intestine Large	intestine
2	chr6:1987400-2003600	Weak transcription	Aorta	Aorta
3	chr6:1988400-1993200	Weak transcription	NH-A	brain
4	chr6:1988400-1993400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:1988400-1993400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:1988400-2008600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:1988600-1993000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:1988600-1993000	Weak transcription	NHEK	skin
9	chr6:1988800-1993000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:1988800-1993200	Weak transcription	HMEC	breast
11	chr6:1988800-1995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:1990200-2008600	Weak transcription	Pancreas	Pancrea
13	chr6:1990400-2010800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:1991200-1994000	Weak transcription	Spleen	Spleen
15	chr6:1991400-1993200	Strong transcription	HepG2	liver
16	chr6:1991800-1993400	Strong transcription	Primary T cells from cord blood	blood
17	chr6:1992000-1993200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr6:1992200-1993400	Weak transcription	Fetal Stomach	stomach
19	chr6:1992600-1993000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:1992600-1993600	Enhancers	Fetal Muscle Leg	muscle
21	chr6:1992800-1993200	Enhancers	Osteobl	bone
22	chr6:1992800-1994400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:1992800-1997800	Weak transcription	Gastric	stomach
24	chr6:1992800-2010200	Weak transcription	Fetal Intestine Small	intestine

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