Variant report

Variant	rs2712248
Chromosome Location	chr7:27120689-27120690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27120424..27122437-chr7:27131942..27133527,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10238645	0.82[EUR][1000 genomes]
rs10242754	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11563327	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs17471061	0.80[EUR][1000 genomes]
rs17471088	0.86[EUR][1000 genomes]
rs2079138	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2248744	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2253415	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs2254463	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2264802	0.82[EUR][1000 genomes]
rs2428416	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2428417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2428418	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2428421	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2428425	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2428431	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2462900	0.81[EUR][1000 genomes]
rs2462902	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2462906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462908	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465264	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2465266	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2465270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2465274	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2522824	1.00[ASW][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap]
rs2522825	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2522826	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2648076	0.81[EUR][1000 genomes]
rs2693659	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2693665	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2693668	0.82[EUR][1000 genomes]
rs2712234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2712242	1.00[ASW][hapmap];0.83[CEU][hapmap];0.88[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap]
rs2712246	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs34725546	0.84[ASN][1000 genomes]
rs55889667	0.82[EUR][1000 genomes]
rs6668	0.81[ASN][1000 genomes]

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	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1018709	chr7:26990384-27216552	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	nsv538806	chr7:26990384-27216552	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv887856	chr7:27073731-27297791	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
6	nsv824038	chr7:27119294-27284522	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
7	nsv887857	chr7:27120689-27229549	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2712248	INMT	cis	parietal	SCAN
rs2712248	C7orf31	cis	parietal	SCAN
rs2712248	HOTAIRM1	cis	Whole Blood	GTEx
rs2712248	HOXA2	cis	Whole Blood	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27118400-27122600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:27118800-27121400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:27118800-27122600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:27118800-27122800	Enhancers	HMEC	breast
5	chr7:27119000-27122600	Enhancers	Hela-S3	cervix
6	chr7:27119200-27121000	Enhancers	HepG2	liver
7	chr7:27119200-27121800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:27119200-27127600	Weak transcription	Osteobl	bone
9	chr7:27119400-27121000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:27119600-27125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:27120000-27121000	Enhancers	Placenta Amnion	Placenta Amnion
12	chr7:27120200-27121000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr7:27120200-27121000	Enhancers	Fetal Intestine Large	intestine
14	chr7:27120400-27120800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:27120400-27120800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr7:27120400-27120800	Flanking Active TSS	A549	lung
17	chr7:27120400-27120800	Flanking Active TSS	NHEK	skin
18	chr7:27120400-27121000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:27120400-27121000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr7:27120400-27121000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
21	chr7:27120400-27121000	Enhancers	HSMM	muscle
22	chr7:27120400-27121400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr7:27120400-27121400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:27120400-27121400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr7:27120400-27121400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr7:27120600-27121000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:27120600-27121000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr7:27120600-27121000	Bivalent Enhancer	Fetal Heart	heart
29	chr7:27120600-27121400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr7:27120600-27121400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr7:27120600-27121400	Enhancers	Fetal Intestine Small	intestine
32	chr7:27120600-27122000	Enhancers	HSMMtube	muscle

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