Variant report

Variant	rs62564446
Chromosome Location	chr9:79066898-79066899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79065522..79068324-chr9:79072541..79074229,2	MCF-7	breast:
2	chr9:79017044..79018975-chr9:79065546..79068177,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10116800	0.84[ASN][1000 genomes]
rs10118954	0.84[ASN][1000 genomes]
rs10125012	0.84[ASN][1000 genomes]
rs10125667	0.84[ASN][1000 genomes]
rs10781358	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10781360	0.84[ASN][1000 genomes]
rs10869770	0.84[ASN][1000 genomes]
rs10869781	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144870	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11144875	0.84[ASN][1000 genomes]
rs11144878	0.84[ASN][1000 genomes]
rs11144881	0.84[ASN][1000 genomes]
rs11144887	0.84[ASN][1000 genomes]
rs11144897	0.83[EUR][1000 genomes]
rs11144905	0.90[ASN][1000 genomes]
rs11144908	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144909	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1129399	0.84[ASN][1000 genomes]
rs11791951	0.84[ASN][1000 genomes]
rs11793613	0.84[ASN][1000 genomes]
rs11794019	0.84[ASN][1000 genomes]
rs12156473	0.84[ASN][1000 genomes]
rs12351617	0.95[ASN][1000 genomes]
rs12377856	0.84[ASN][1000 genomes]
rs12377878	0.84[ASN][1000 genomes]
rs12378822	0.85[ASN][1000 genomes]
rs12380332	1.00[ASN][1000 genomes]
rs1324212	0.90[ASN][1000 genomes]
rs1324213	0.84[ASN][1000 genomes]
rs1951910	0.84[ASN][1000 genomes]
rs2480213	0.90[AMR][1000 genomes]
rs4571791	0.84[ASN][1000 genomes]
rs502417	0.90[AMR][1000 genomes]
rs512269	0.88[AMR][1000 genomes]
rs513301	0.88[AMR][1000 genomes]
rs55740812	0.89[ASN][1000 genomes]
rs57339182	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57429014	0.90[ASN][1000 genomes]
rs57480680	0.84[ASN][1000 genomes]
rs58651349	0.95[ASN][1000 genomes]
rs59322809	0.95[ASN][1000 genomes]
rs602075	0.88[AMR][1000 genomes]
rs62564444	0.90[ASN][1000 genomes]
rs62564449	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62564454	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62565109	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62567918	0.89[ASN][1000 genomes]
rs62568690	0.84[ASN][1000 genomes]
rs62568692	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6560516	0.84[ASN][1000 genomes]
rs6560524	0.95[ASN][1000 genomes]
rs7025942	0.84[ASN][1000 genomes]
rs7026067	0.84[ASN][1000 genomes]
rs7029439	0.84[ASN][1000 genomes]
rs7035385	0.84[ASN][1000 genomes]
rs7038009	0.84[ASN][1000 genomes]
rs7040138	0.84[ASN][1000 genomes]
rs7041690	0.84[ASN][1000 genomes]
rs7047489	0.84[ASN][1000 genomes]
rs7049245	0.84[ASN][1000 genomes]
rs7851616	0.84[ASN][1000 genomes]
rs7852884	0.84[ASN][1000 genomes]
rs7853410	0.84[ASN][1000 genomes]
rs7854540	1.00[ASN][1000 genomes]
rs785914	0.85[AMR][1000 genomes]
rs785915	0.85[AMR][1000 genomes]
rs785916	0.85[AMR][1000 genomes]
rs7859327	0.84[ASN][1000 genomes]
rs7875575	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	esv1558364	chr9:79066897-79066900	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62564446	RFK	cis	brain	BrainEAC

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79063000-79067400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:79063000-79068000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:79063000-79070800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr9:79063400-79068000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:79063600-79067800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:79064200-79067600	Weak transcription	Fetal Brain Male	brain
7	chr9:79064400-79067200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr9:79064600-79071000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:79065000-79067000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr9:79065200-79067000	Enhancers	HSMM	muscle
11	chr9:79065200-79069200	Enhancers	NHDF-Ad	bronchial
12	chr9:79065400-79067000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:79065400-79067000	Enhancers	Osteobl	bone
14	chr9:79066200-79067200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:79066200-79071000	Weak transcription	A549	lung
16	chr9:79066400-79067400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr9:79066400-79067400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:79066400-79067600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr9:79066400-79068600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:79066600-79070800	Weak transcription	HSMMtube	muscle
21	chr9:79066600-79073600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:79066800-79067400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:79066800-79067800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:79066800-79068400	Weak transcription	NHLF	lung
25	chr9:79066800-79070800	Weak transcription	NH-A	brain
26	chr9:79066800-79071000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:79066800-79071200	Weak transcription	HMEC	breast

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