Variant report

Variant	rs12204653
Chromosome Location	chr6:150213021-150213022
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150183161..150188305-chr6:150206346..150214162,9	MCF-7	breast:
2	chr6:150212160..150213980-chr6:150214968..150218117,3	K562	blood:

Variant related genes	Relation type
ENSG00000164520	Chromatin interaction
ENSG00000120256	Chromatin interaction
ENSG00000268592	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10457852	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12209310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12210822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12527391	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12528243	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1855572	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1999632	0.94[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1999633	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2342766	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922946	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3922947	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4473864	0.84[ASN][1000 genomes]
rs4869755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869767	0.94[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4869768	0.94[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4870078	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4870110	0.84[ASN][1000 genomes]
rs4870117	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4870118	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5024811	0.94[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57894361	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6557165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6912330	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6925151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7452592	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7764677	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs915140	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9322229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9371228	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9383941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9397070	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]

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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12204653	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs12204653	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs12204653	RAET1G	cis	Thyroid	GTEx
rs12204653	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs12204653	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs12204653	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs12204653	RP11-350J20.5	cis	lung	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150205600-150216000	Weak transcription	Right Atrium	heart
2	chr6:150205800-150216000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:150206000-150216000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:150209600-150215800	Weak transcription	Adipose Nuclei	Adipose
5	chr6:150209600-150216000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:150209600-150222200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:150212000-150213200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:150212000-150216000	Weak transcription	Placenta	Placenta
9	chr6:150212000-150216000	Weak transcription	Lung	lung
10	chr6:150212000-150216000	Weak transcription	Ovary	ovary
11	chr6:150212000-150216000	Weak transcription	Psoas Muscle	Psoas
12	chr6:150212000-150216200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:150212200-150213200	Enhancers	HMEC	breast
14	chr6:150212200-150215800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:150212200-150215800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:150212400-150216200	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:150212600-150215800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:150212600-150216000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:150212600-150216000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:150212600-150216000	Weak transcription	Esophagus	oesophagus
21	chr6:150212600-150216200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:150212600-150216200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:150212600-150216200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:150212600-150216200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:150212600-150216400	Weak transcription	HSMMtube	muscle
26	chr6:150212800-150215800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:150212800-150215800	Weak transcription	A549	lung
28	chr6:150212800-150215800	Weak transcription	Hela-S3	cervix
29	chr6:150212800-150215800	Weak transcription	NHDF-Ad	bronchial
30	chr6:150212800-150215800	Weak transcription	NHEK	skin
31	chr6:150212800-150216000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:150212800-150216200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:150212800-150216200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:150212800-150216400	Weak transcription	Osteobl	bone
35	chr6:150212800-150216600	Weak transcription	HSMM	muscle

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