Variant report

Variant	rs12529458
Chromosome Location	chr6:27361681-27361682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27356549..27360030-chr6:27360597..27364786,4	MCF-7	breast:
2	chr6:27360610..27362921-chr6:27368248..27371052,2	MCF-7	breast:
3	chr6:27355433..27358634-chr6:27358913..27363136,5	K562	blood:

Variant related genes	Relation type
ENSG00000124613	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1011665	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10946915	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12526495	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12663650	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12664996	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220817	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs1883403	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs2064093	0.86[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs2206250	0.81[CHD][hapmap]
rs2235232	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2393926	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2393962	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap]
rs2393964	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs4711152	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713098	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4713099	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6913166	0.98[GIH][hapmap];0.97[ASN][1000 genomes]
rs6914864	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6922815	0.83[ASN][1000 genomes]
rs71559025	0.85[ASN][1000 genomes]
rs764284	0.92[ASN][1000 genomes]
rs7761966	0.86[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs7772160	0.89[YRI][hapmap]
rs7772739	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357038	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379980	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9393813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1031803	chr6:27355881-27423655	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538166	chr6:27355881-27423655	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv5235	chr6:27358498-27404074	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12529458	BTN3A3	cis	cerebellum	SCAN
rs12529458	ZNF204P	cis	cerebellum	SCAN
rs12529458	ZNF391	cis	Skin Sun Exposed Lower leg	GTEx
rs12529458	ZNF391	cis	cerebellum	SCAN
rs12529458	ZNF204P	cis	parietal	SCAN
rs12529458	ZNF391	cis	lung	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27357200-27362200	Weak transcription	Aorta	Aorta
2	chr6:27357200-27366600	Weak transcription	Left Ventricle	heart
3	chr6:27357400-27363000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:27357400-27363000	Weak transcription	Right Atrium	heart
5	chr6:27357400-27364200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:27357400-27364800	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:27357400-27364800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:27357400-27365000	Weak transcription	Fetal Lung	lung
9	chr6:27357400-27366000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:27357400-27367000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:27357400-27367200	Weak transcription	Brain Substantia Nigra	brain
12	chr6:27357400-27367800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:27357400-27368000	Weak transcription	Fetal Kidney	kidney
14	chr6:27357600-27362000	Weak transcription	Fetal Stomach	stomach
15	chr6:27357600-27362000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr6:27357600-27362800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:27357600-27365000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:27357600-27365000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:27357600-27365800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:27357600-27367000	Weak transcription	Fetal Brain Male	brain
21	chr6:27357600-27368000	Weak transcription	Brain Angular Gyrus	brain
22	chr6:27357600-27368600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:27357600-27368800	Weak transcription	Pancreas	Pancrea
24	chr6:27357800-27362000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:27357800-27362800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:27357800-27366800	Weak transcription	Brain Anterior Caudate	brain
27	chr6:27357800-27367000	Weak transcription	Spleen	Spleen
28	chr6:27357800-27367200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:27358000-27365000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:27358000-27367000	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:27358000-27368200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:27358200-27363000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:27359600-27371200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:27359600-27372200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:27360000-27371400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
36	chr6:27360200-27362000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:27360600-27370800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:27361000-27362400	Enhancers	Adipose Nuclei	Adipose
39	chr6:27361600-27362000	Weak transcription	H9 Cell Line	embryonic stem cell

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