Variant report

Variant	rs12201039
Chromosome Location	chr6:57018969-57018970
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	chr6:57011547..57015290-chr6:57018812..57021897,3	MCF-7	breast:
2	chr6:57017995..57019837-chr6:57028453..57031266,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1020550	0.80[ASN][1000 genomes]
rs1044670	0.81[AFR][1000 genomes]
rs10456192	0.83[EUR][1000 genomes]
rs10484410	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11398	1.00[ASN][1000 genomes]
rs12190575	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12192222	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12194288	1.00[ASN][1000 genomes]
rs12194407	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12198801	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211901	1.00[ASN][1000 genomes]
rs12214119	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12214882	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1411578	1.00[ASN][1000 genomes]
rs1547226	0.80[ASN][1000 genomes]
rs16888392	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17619360	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3800018	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800023	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3800025	0.80[ASN][1000 genomes]
rs3957366	0.90[AFR][1000 genomes]
rs3996934	0.80[ASN][1000 genomes]
rs3996935	0.80[ASN][1000 genomes]
rs3996936	0.80[ASN][1000 genomes]
rs41267681	0.81[AFR][1000 genomes]
rs4523090	0.80[ASN][1000 genomes]
rs4631287	0.80[ASN][1000 genomes]
rs6459178	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6918222	0.90[AFR][1000 genomes]
rs6936506	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6936560	0.81[AFR][1000 genomes]
rs72868608	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744148	0.80[ASN][1000 genomes]
rs7748120	0.80[ASN][1000 genomes]
rs7748453	0.80[ASN][1000 genomes]
rs7753547	0.80[ASN][1000 genomes]
rs7756421	0.98[EUR][1000 genomes]
rs7764446	0.80[ASN][1000 genomes]
rs7771115	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9396256	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12201039	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs12201039	BEND6	cis	Muscle Skeletal	GTEx
rs12201039	RAB23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56968200-57036400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:56985600-57036800	Weak transcription	Pancreas	Pancrea
3	chr6:56991600-57036600	Weak transcription	Small Intestine	intestine
4	chr6:56995800-57036600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:56996000-57036800	Weak transcription	Gastric	stomach
6	chr6:56996200-57036600	Weak transcription	Fetal Brain Male	brain
7	chr6:56996400-57036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:56998800-57027400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:56999800-57036600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:57001200-57036600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:57002600-57036600	Weak transcription	A549	lung
12	chr6:57005600-57021600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:57005600-57023400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:57005600-57023800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:57005800-57022400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:57006200-57028600	Strong transcription	Liver	Liver
17	chr6:57006600-57021600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:57006600-57036600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:57008400-57022000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:57010000-57021400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:57010800-57024600	Strong transcription	Primary B cells from cord blood	blood
22	chr6:57011400-57020000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:57011400-57020000	Strong transcription	HepG2	liver
24	chr6:57011400-57021400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr6:57011400-57036600	Weak transcription	Stomach Mucosa	stomach
26	chr6:57011800-57021400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:57011800-57023000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:57012000-57021600	Strong transcription	Primary T cells from cord blood	blood
29	chr6:57012400-57036800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:57012800-57021600	Weak transcription	Esophagus	oesophagus
31	chr6:57012800-57036400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:57012800-57036600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:57013000-57029000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:57013200-57036600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:57013400-57023800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:57013400-57027000	Weak transcription	Hela-S3	cervix
37	chr6:57013400-57027200	Weak transcription	NHLF	lung
38	chr6:57013600-57020600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr6:57013600-57036000	Weak transcription	Fetal Heart	heart
40	chr6:57014600-57022400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr6:57014600-57029000	Weak transcription	Fetal Kidney	kidney
42	chr6:57014800-57020000	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr6:57015000-57020200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:57015000-57021400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr6:57015000-57021600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:57015000-57021600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:57015000-57021600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr6:57015200-57019400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:57015200-57020600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:57015200-57021000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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