Variant report

Variant	rs2568045
Chromosome Location	chr11:9004060-9004061
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	chr11:8986277..8988105-chr11:9002713..9005054,2	K562	blood:
2	chr11:8991559..8993834-chr11:9003227..9005288,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175348	Chromatin interaction
ENSG00000254860	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10743093	0.84[CEU][hapmap]
rs10769967	0.85[CEU][hapmap]
rs10769970	0.85[CEU][hapmap]
rs10769973	0.85[CEU][hapmap]
rs10769979	0.93[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs10769980	0.82[EUR][1000 genomes]
rs10840134	0.84[CEU][hapmap]
rs10840135	0.83[JPT][hapmap]
rs10840141	0.85[CEU][hapmap]
rs10840142	0.85[CEU][hapmap]
rs10840147	0.89[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs10840148	0.85[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs10840157	0.81[EUR][1000 genomes]
rs10840158	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042078	0.81[CEU][hapmap]
rs11042103	0.85[CEU][hapmap]
rs11042104	0.83[JPT][hapmap]
rs11042125	0.85[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap]
rs11042149	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042150	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042151	0.93[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs11042152	0.81[EUR][1000 genomes]
rs11042154	0.93[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs1123936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603841	0.87[CEU][hapmap]
rs1368017	0.83[JPT][hapmap]
rs1529641	0.82[CEU][hapmap]
rs1560569	0.93[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap]
rs16906256	0.83[JPT][hapmap]
rs1980428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980429	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2012680	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2012690	0.97[EUR][1000 genomes]
rs2012696	0.81[EUR][1000 genomes]
rs2016942	0.93[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap]
rs2568020	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2568043	0.84[CEU][hapmap]
rs2568061	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap]
rs2568065	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap]
rs2568090	0.85[CEU][hapmap]
rs2653570	0.96[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2653605	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2742470	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742471	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2742474	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2742480	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2742536	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap]
rs2742537	0.91[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap]
rs2742540	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap]
rs2742545	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2742552	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap]
rs4909952	0.92[CEU][hapmap]
rs4910062	0.83[CEU][hapmap]
rs4910157	0.84[EUR][1000 genomes]
rs4910442	0.84[CEU][hapmap]
rs4929922	0.90[GIH][hapmap];0.87[MEX][hapmap]
rs6486060	0.85[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs7119939	0.84[CEU][hapmap]
rs7123429	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs7479407	0.93[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs7482838	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7484180	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7925728	0.93[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7930026	0.92[CEU][hapmap]
rs7937298	0.85[CEU][hapmap]
rs7945705	0.85[CEU][hapmap]

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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2568045	OR52A1	cis	parietal	SCAN
rs2568045	TMEM9B-AS1	cis	Artery Aorta	GTEx
rs2568045	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs2568045	TMEM9B-AS1	cis	lung	GTEx
rs2568045	RPL27A	cis	parietal	SCAN
rs2568045	NRIP3	cis	parietal	SCAN
rs2568045	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2568045	TMEM9B-AS1	cis	Thyroid	GTEx
rs2568045	RRP8	cis	parietal	SCAN
rs2568045	TMEM9B-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8987000-9007200	Weak transcription	Brain Germinal Matrix	brain
2	chr11:8987000-9007200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:8987000-9010200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:8987000-9011000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:8987600-9005000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:8987600-9006400	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:8987600-9010000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:8987600-9010000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr11:8987800-9005000	Weak transcription	Brain Angular Gyrus	brain
10	chr11:8987800-9010200	Weak transcription	NHDF-Ad	bronchial
11	chr11:8987800-9012000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:8989600-9010000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:8989600-9011200	Weak transcription	Brain Anterior Caudate	brain
14	chr11:8989600-9019600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:8991800-9015600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:8994000-9008600	Weak transcription	K562	blood
17	chr11:8996400-9005800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:8999600-9009800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:9001800-9004400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:9001800-9015200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:9002200-9004200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:9004000-9004400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:9004000-9006600	Weak transcription	HepG2	liver

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