Variant report

Variant	rs2096345
Chromosome Location	chr1:223841682-223841683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223833118..223836523-chr1:223838327..223841763,4	MCF-7	breast:
2	chr1:223840282..223843675-chr1:223851675..223856291,7	MCF-7	breast:
3	chr1:223840874..223841758-chr8:63546888..63547676,2	MCF-7	breast:
4	chr1:223836208..223847031-chr1:223849408..223858826,22	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203697	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10737417	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10799583	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10915755	1.00[CEU][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10915858	1.00[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10915937	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1108088	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12059740	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12127418	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12405993	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2105405	1.00[ASW][hapmap];1.00[CEU][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]
rs2105406	0.94[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs7516954	0.82[ASW][hapmap];0.85[LWK][hapmap];0.83[YRI][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	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv873209	chr1:223707647-223846564	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv873210	chr1:223707647-223856414	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv873211	chr1:223707647-223867631	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1000199	chr1:223803545-223854859	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv873212	chr1:223807262-223853792	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1012050	chr1:223824652-223843610	Weak transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv535309	chr1:223824652-223843610	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2096345	TGFB2	cis	cerebellum	SCAN
rs2096345	BPNT1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223830400-223841800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:223833600-223850800	Weak transcription	Colonic Mucosa	Colon
3	chr1:223834200-223841800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:223838200-223842600	Weak transcription	Lung	lung
5	chr1:223838200-223850800	Weak transcription	Fetal Stomach	stomach
6	chr1:223839200-223841800	Enhancers	Fetal Brain Male	brain
7	chr1:223839200-223843600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:223839600-223841800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:223839600-223843000	Weak transcription	Fetal Intestine Large	intestine
10	chr1:223840000-223843600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:223840200-223841800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr1:223840600-223841800	Weak transcription	Esophagus	oesophagus
13	chr1:223840600-223843000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:223840600-223843400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:223840600-223853200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:223840800-223841800	Weak transcription	Fetal Lung	lung
17	chr1:223840800-223841800	Weak transcription	Psoas Muscle	Psoas
18	chr1:223840800-223843400	Enhancers	NHEK	skin
19	chr1:223840800-223843600	Enhancers	Stomach Mucosa	stomach
20	chr1:223841000-223841800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:223841000-223842000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:223841000-223842000	Weak transcription	Gastric	stomach
23	chr1:223841000-223842800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:223841000-223843000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:223841000-223843800	Enhancers	HMEC	breast
26	chr1:223841200-223841800	Enhancers	Fetal Brain Female	brain
27	chr1:223841600-223842200	Flanking Active TSS	A549	lung
28	chr1:223841600-223842200	Enhancers	HepG2	liver
29	chr1:223841600-223843000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr1:223841600-223843800	Enhancers	Duodenum Mucosa	Duodenum
31	chr1:223841600-223843800	Enhancers	Rectal Mucosa Donor 31	rectum

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