Variant report

Variant	rs2230585
Chromosome Location	chr7:100410597-100410598
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	chr7:100410343..100413835-chr7:100422249..100426210,7	MCF-7	breast:
2	chr7:100404960..100406737-chr7:100409300..100411375,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146828	Chromatin interaction
ENSG00000196411	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs144173	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs221804	0.83[EUR][1000 genomes]
rs2247445	0.80[JPT][hapmap]
rs2250818	0.80[JPT][hapmap]
rs2406146	0.92[EUR][1000 genomes]
rs2472559	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2571607	0.80[JPT][hapmap]
rs314309	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs314310	0.96[CEU][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs314341	0.86[EUR][1000 genomes]
rs314343	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs314344	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs314347	0.89[EUR][1000 genomes]
rs314353	0.96[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs314356	0.96[CEU][hapmap]
rs314357	0.96[EUR][1000 genomes]
rs314358	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs314359	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs482308	0.88[CEU][hapmap]
rs489951	0.88[CEU][hapmap];0.88[GIH][hapmap]
rs531503	0.88[CEU][hapmap];0.87[GIH][hapmap]
rs539445	0.88[CEU][hapmap]
rs540330	0.80[CEU][hapmap]
rs542137	0.88[CEU][hapmap]
rs7794532	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv888796	chr7:100313420-100423365	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
9	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
10	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
11	nsv888797	chr7:100386900-100482026	Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
12	nsv888798	chr7:100406144-100472826	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
13	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
14	nsv967435	chr7:100406273-100422961	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2230585	MCM7	cis	cerebellum	SCAN
rs2230585	VGF	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100399600-100422200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:100399600-100422200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:100399800-100422400	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr7:100399800-100422400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:100400000-100422200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:100400400-100422200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr7:100401600-100410800	Weak transcription	Osteobl	bone
8	chr7:100401600-100420800	Weak transcription	Brain Angular Gyrus	brain
9	chr7:100401600-100421800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:100401600-100421800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:100401600-100422000	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr7:100401600-100422000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:100401600-100422600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr7:100401600-100423200	Weak transcription	Brain Anterior Caudate	brain
15	chr7:100401800-100410600	Weak transcription	Hela-S3	cervix
16	chr7:100401800-100411000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr7:100401800-100411200	Weak transcription	Brain Hippocampus Middle	brain
18	chr7:100401800-100411400	Weak transcription	Primary B cells from cord blood	blood
19	chr7:100401800-100412200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr7:100401800-100412200	Strong transcription	HMEC	breast
21	chr7:100401800-100413400	Weak transcription	Brain Substantia Nigra	brain
22	chr7:100401800-100415800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr7:100401800-100416600	Weak transcription	Stomach Mucosa	stomach
24	chr7:100401800-100419600	Weak transcription	Right Atrium	heart
25	chr7:100401800-100421400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:100401800-100421400	Strong transcription	Fetal Stomach	stomach
27	chr7:100401800-100422200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr7:100401800-100422200	Weak transcription	Fetal Heart	heart
29	chr7:100401800-100422400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr7:100401800-100422400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr7:100401800-100422400	Strong transcription	Fetal Intestine Large	intestine
32	chr7:100401800-100422600	Weak transcription	Fetal Brain Male	brain
33	chr7:100401800-100422600	Strong transcription	Fetal Intestine Small	intestine
34	chr7:100401800-100423000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:100402000-100411600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:100402000-100421200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr7:100402000-100421800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr7:100402000-100421800	Strong transcription	NHEK	skin
39	chr7:100402000-100422000	Strong transcription	Fetal Muscle Leg	muscle
40	chr7:100402000-100422600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:100402000-100422600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr7:100402200-100413400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr7:100402200-100418400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr7:100402200-100418600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr7:100402200-100421600	Strong transcription	Adipose Nuclei	Adipose
46	chr7:100402200-100421600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr7:100402200-100421800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:100402400-100419000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr7:100402400-100422000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr7:100402400-100422000	Strong transcription	Fetal Lung	lung

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