Variant report

Variant	rs12780246
Chromosome Location	chr10:5898205-5898206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5853185..5855023-chr10:5896110..5898472,2	K562	blood:
2	chr10:5855459..5857550-chr10:5896557..5898407,2	K562	blood:
3	chr10:5853523..5857550-chr10:5895504..5898472,4	K562	blood:

Variant related genes	Relation type
ENSG00000057608	Chromatin interaction
ENSG00000272764	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10508298	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10508299	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10752281	1.00[JPT][hapmap]
rs10905316	0.80[EUR][1000 genomes]
rs11255527	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11255548	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11255564	0.80[EUR][1000 genomes]
rs11255577	0.81[EUR][1000 genomes]
rs11255581	0.83[EUR][1000 genomes]
rs11255662	0.88[AFR][1000 genomes]
rs11255780	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs11255974	1.00[CHB][hapmap]
rs11524382	0.80[EUR][1000 genomes]
rs11819695	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12255077	0.81[EUR][1000 genomes]
rs12359234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360409	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12769593	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774228	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12774886	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12774966	0.82[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs12777477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12779398	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12784539	0.81[EUR][1000 genomes]
rs12785055	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17319759	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2203197	0.82[MEX][hapmap];0.85[TSI][hapmap]
rs2380201	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2380205	0.82[MEX][hapmap];0.87[TSI][hapmap]
rs2380208	0.82[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs2387092	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3209286	1.00[JPT][hapmap]
rs4293038	0.81[EUR][1000 genomes]
rs4301704	0.80[EUR][1000 genomes]
rs4330991	0.81[EUR][1000 genomes]
rs4428973	0.82[EUR][1000 genomes]
rs4468244	0.80[EUR][1000 genomes]
rs4497300	0.81[EUR][1000 genomes]
rs6602330	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs6602819	1.00[JPT][hapmap]
rs7067928	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7072174	0.82[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs7073128	0.80[EUR][1000 genomes]
rs7082434	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs7090411	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7098372	0.82[MEX][hapmap];0.87[TSI][hapmap]
rs7099029	0.80[EUR][1000 genomes]
rs7893735	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7894083	0.82[MEX][hapmap];0.87[TSI][hapmap]
rs7915822	0.90[ASN][1000 genomes]
rs7919913	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs867053	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs907685	0.82[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs907686	0.87[TSI][hapmap]
rs907688	0.82[MEX][hapmap];0.87[TSI][hapmap]
rs907689	0.82[MEX][hapmap];0.85[TSI][hapmap]
rs907690	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9424204	1.00[JPT][hapmap]
rs9663697	0.80[EUR][1000 genomes]
rs9663995	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv5654	chr10:5868365-5930634	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3342274	chr10:5875995-5901345	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv1801910	chr10:5881740-5898882	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	esv1807017	chr10:5890688-5898882	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv466722	chr10:5893268-5916201	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv549904	chr10:5893268-5916201	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12780246	ANKRD16	cis	parietal	SCAN
rs12780246	ANKRD16	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5888800-5904400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:5889200-5900400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr10:5889400-5902000	Weak transcription	Placenta	Placenta
4	chr10:5894600-5908600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr10:5894600-5908600	Weak transcription	K562	blood
6	chr10:5894600-5916800	Weak transcription	Spleen	Spleen
7	chr10:5896200-5912200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr10:5896400-5898400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr10:5896400-5899800	Weak transcription	Brain Anterior Caudate	brain
10	chr10:5896400-5899800	Weak transcription	Brain Substantia Nigra	brain
11	chr10:5896400-5900200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:5896400-5918200	Weak transcription	Fetal Lung	lung
13	chr10:5896600-5902000	Weak transcription	Fetal Muscle Leg	muscle
14	chr10:5896600-5903800	Weak transcription	Fetal Stomach	stomach
15	chr10:5897000-5903800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr10:5897200-5898400	Enhancers	HepG2	liver
17	chr10:5898200-5899000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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