Variant report

Variant	rs1389690
Chromosome Location	chr8:104177331-104177332
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:104162104..104164227-chr8:104176288..104178946,2	MCF-7	breast:
2	chr8:104174608..104177448-chr8:104227251..104229370,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10099640	1.00[AFR][1000 genomes]
rs10110129	1.00[ASN][1000 genomes]
rs10111507	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10112046	1.00[ASN][1000 genomes]
rs10113161	1.00[ASN][1000 genomes]
rs10113728	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs1032471	1.00[CHD][hapmap]
rs10481102	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774996	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11784151	1.00[ASN][1000 genomes]
rs11785583	1.00[CHD][hapmap]
rs13255229	1.00[ASN][1000 genomes]
rs13262291	1.00[ASN][1000 genomes]
rs13275173	1.00[ASN][1000 genomes]
rs13439041	1.00[ASN][1000 genomes]
rs1494282	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17204757	1.00[ASN][1000 genomes]
rs17793532	1.00[ASN][1000 genomes]
rs28495148	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28709120	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28735228	1.00[ASN][1000 genomes]
rs6990501	1.00[CHD][hapmap]
rs728909	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827528	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831413	chr8:104085141-104269789	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1389690	TM7SF4	cis	cerebellum	SCAN
rs1389690	FZD6	cis	parietal	SCAN
rs1389690	FZD6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104166200-104179800	Weak transcription	Spleen	Spleen
2	chr8:104166600-104178800	Weak transcription	Fetal Brain Male	brain
3	chr8:104169400-104177600	Weak transcription	Brain Angular Gyrus	brain
4	chr8:104172600-104178000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr8:104174400-104177400	Weak transcription	Aorta	Aorta
6	chr8:104175200-104178800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr8:104175400-104177600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr8:104176000-104179800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr8:104176600-104177400	Strong transcription	Primary hematopoietic stem cells	blood
10	chr8:104176600-104177800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:104176600-104178200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr8:104176600-104178800	Enhancers	Brain Anterior Caudate	brain
13	chr8:104176600-104179200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr8:104176800-104178400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr8:104176800-104178400	Enhancers	Brain Hippocampus Middle	brain
16	chr8:104177000-104177600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr8:104177000-104177600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr8:104177000-104177600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr8:104177000-104178000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr8:104177000-104178000	Weak transcription	Osteobl	bone
21	chr8:104177000-104178200	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr8:104177000-104178400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr8:104177000-104178400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr8:104177000-104178400	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr8:104177000-104178400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr8:104177000-104178600	Enhancers	Brain Substantia Nigra	brain
27	chr8:104177000-104179600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr8:104177200-104177600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr8:104177200-104177600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr8:104177200-104177600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr8:104177200-104177600	Enhancers	Lung	lung
32	chr8:104177200-104178800	Enhancers	Brain Cingulate Gyrus	brain

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