Variant report

Variant	rs2240389
Chromosome Location	chr7:101256833-101256834
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	chr7:101255927..101262461-chr7:101262750..101268268,7	MCF-7	breast:
2	chr7:101252945..101257038-chr7:101259636..101262173,3	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12532732	0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12533518	0.97[ASN][1000 genomes]
rs12540150	1.00[ASN][1000 genomes]
rs13226908	0.99[ASN][1000 genomes]
rs2240390	1.00[ASN][1000 genomes]
rs4727501	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6465819	0.92[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap]
rs6960162	0.92[CHB][hapmap];0.80[CHD][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv888821	chr7:101091470-101311540	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv831078	chr7:101094945-101257486	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv888822	chr7:101105017-101330734	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv888824	chr7:101109073-101330734	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv888825	chr7:101168283-101330734	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1018544	chr7:101225639-101424889	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv539045	chr7:101225639-101424889	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv888826	chr7:101230768-101277334	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv482758	chr7:101231458-101395219	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2240389	MGC72080	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101252600-101257800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:101252800-101257200	Weak transcription	Placenta	Placenta
3	chr7:101252800-101257800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:101252800-101257800	Weak transcription	HMEC	breast
5	chr7:101252800-101258000	Weak transcription	Right Atrium	heart
6	chr7:101252800-101260800	Weak transcription	Esophagus	oesophagus
7	chr7:101256200-101257000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr7:101256200-101257000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr7:101256200-101257000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr7:101256200-101257200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr7:101256200-101258600	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr7:101256200-101258800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr7:101256200-101258800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr7:101256200-101258800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:101256200-101259000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:101256200-101259400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:101256200-101259600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr7:101256200-101259600	Enhancers	Fetal Muscle Leg	muscle
19	chr7:101256400-101257000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr7:101256400-101257000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:101256400-101258800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr7:101256400-101258800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:101256600-101257000	Enhancers	Fetal Brain Female	brain
24	chr7:101256600-101257200	Enhancers	H9 Cell Line	embryonic stem cell
25	chr7:101256600-101257600	Enhancers	Aorta	Aorta
26	chr7:101256600-101258200	Weak transcription	Gastric	stomach
27	chr7:101256800-101257800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr7:101256800-101257800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr7:101256800-101257800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr7:101256800-101258400	Weak transcription	Ovary	ovary
31	chr7:101256800-101258600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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