Variant report

Variant	rs9469953
Chromosome Location	chr6:35129816-35129817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35118855..35121667-chr6:35128574..35130894,2	MCF-7	breast:
2	chr6:35127079..35138793-chr6:35145525..35157743,32	MCF-7	breast:
3	chr6:35126225..35131731-chr6:35132022..35136988,7	MCF-7	breast:
4	chr6:35115116..35116634-chr6:35129312..35132110,2	MCF-7	breast:
5	chr6:35129806..35132792-chr6:35197170..35199424,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANKS1A-1	chr6:35127447-35132003	ENSG00000244904

Variant related genes	Relation type
ENSG00000124678	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10080361	0.83[CHB][hapmap]
rs10755687	0.90[GIH][hapmap]
rs10807150	0.90[GIH][hapmap]
rs10947540	0.83[CHB][hapmap];0.95[GIH][hapmap]
rs1194	0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap]
rs13214290	0.83[CHB][hapmap];0.95[GIH][hapmap]
rs1557567	0.95[GIH][hapmap]
rs1557568	0.95[GIH][hapmap]
rs1888822	0.95[GIH][hapmap]
rs1888823	0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap]
rs1888824	0.83[CHB][hapmap];0.95[GIH][hapmap]
rs1888825	0.83[CHB][hapmap];0.90[GIH][hapmap]
rs1894650	0.83[CHB][hapmap]
rs1929847	0.83[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap]
rs1929849	0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap]
rs1987673	0.95[GIH][hapmap]
rs2071920	0.95[GIH][hapmap]
rs2267657	0.95[GIH][hapmap]
rs2267662	0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap]
rs2267663	0.83[CHB][hapmap]
rs28522747	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800385	0.83[CHB][hapmap];0.95[GIH][hapmap]
rs4711411	0.83[CHB][hapmap];0.95[GIH][hapmap]
rs4713840	0.94[ASN][1000 genomes]
rs4713845	0.83[CHB][hapmap]
rs55974914	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56154344	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457807	0.97[ASN][1000 genomes]
rs6902523	0.83[CHB][hapmap]
rs6913037	0.83[CHB][hapmap]
rs6933979	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934818	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938946	0.89[CHB][hapmap]
rs914547	0.83[CHB][hapmap];0.95[GIH][hapmap]
rs9296144	0.83[CHB][hapmap]
rs9366880	0.98[ASN][1000 genomes]
rs9366883	0.83[CHB][hapmap]
rs9368851	0.97[ASN][1000 genomes]
rs9380501	0.83[CHB][hapmap]
rs9394278	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9394279	0.98[ASN][1000 genomes]
rs9394288	0.83[CHB][hapmap]
rs9469955	0.97[ASN][1000 genomes]
rs9469964	0.83[CHB][hapmap];0.95[GIH][hapmap]
rs9469972	0.95[GIH][hapmap]
rs975496	0.83[CHB][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9469953	BRPF3	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35118600-35132200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:35127600-35130600	Enhancers	Adipose Nuclei	Adipose
3	chr6:35127600-35130800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:35128200-35130000	Enhancers	Fetal Stomach	stomach
5	chr6:35128200-35130400	Enhancers	Fetal Kidney	kidney
6	chr6:35128200-35130400	Enhancers	HUVEC	blood vessel
7	chr6:35128600-35130200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:35128600-35130800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:35128600-35130800	Weak transcription	Right Atrium	heart
10	chr6:35128600-35130800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:35128600-35133200	Weak transcription	Esophagus	oesophagus
12	chr6:35128600-35133800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:35128600-35137400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:35128800-35130400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:35128800-35137400	Weak transcription	Brain Angular Gyrus	brain
16	chr6:35129000-35130600	Enhancers	Stomach Mucosa	stomach
17	chr6:35129000-35130600	Enhancers	NHDF-Ad	bronchial
18	chr6:35129200-35130200	Enhancers	Aorta	Aorta
19	chr6:35129200-35130600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr6:35129200-35130600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:35129200-35130600	Weak transcription	Spleen	Spleen
22	chr6:35129200-35130600	Enhancers	Osteobl	bone
23	chr6:35129200-35133200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:35129400-35130200	Flanking Active TSS	Liver	Liver
25	chr6:35129600-35130000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:35129600-35130800	Flanking Active TSS	HepG2	liver
27	chr6:35129800-35130000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:35129800-35130000	Bivalent Enhancer	Fetal Muscle Leg	muscle
29	chr6:35129800-35130000	Enhancers	Lung	lung
30	chr6:35129800-35130200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:35129800-35130400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:35129800-35130600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr6:35129800-35130800	Enhancers	Fetal Lung	lung
34	chr6:35129800-35130800	Enhancers	Left Ventricle	heart
35	chr6:35129800-35130800	Enhancers	Right Ventricle	heart
36	chr6:35129800-35131000	Enhancers	Pancreas	Pancrea

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