Variant report

Variant	rs957828
Chromosome Location	chr1:84541716-84541717
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:84540833-84542144	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:84387778..84389882-chr1:84541236..84543359,2	K562	blood:
2	chr1:84540590..84543508-chr1:84558962..84560991,2	K562	blood:
3	chr1:84413047..84415136-chr1:84540240..84542127,2	K562	blood:
4	chr1:84541598..84548799-chr1:84549003..84554628,15	K562	blood:
5	chr1:84539350..84542065-chr1:84568304..84570726,2	K562	blood:
6	chr1:84539639..84541968-chr1:84547734..84550751,3	K562	blood:
7	chr1:84411907..84414547-chr1:84539636..84541740,2	K562	blood:
8	chr1:84540791..84543154-chr1:84633401..84635166,2	K562	blood:
9	chr1:84541371..84543109-chr1:84583953..84586517,2	K562	blood:

No data

Variant related genes	Relation type
PRKACB	TF binding region
ENSG00000137941	Chromatin interaction
ENSG00000213540	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10493750	0.80[JPT][hapmap]
rs10782822	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10874427	0.80[MEX][hapmap]
rs11163897	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11163898	0.80[JPT][hapmap]
rs11163900	0.80[JPT][hapmap]
rs12405120	0.80[JPT][hapmap]
rs12724598	0.80[JPT][hapmap]
rs12746741	0.83[JPT][hapmap]
rs2792975	0.86[CHB][hapmap]
rs3861699	0.85[JPT][hapmap]
rs4907193	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6674038	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6703653	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7520283	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.90[AMR][1000 genomes];0.93[ASN][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	nsv1732	chr1:84499098-84544635	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv871655	chr1:84517261-84550849	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv3379138	chr1:84531980-84545128	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs957828	MCOLN2	cis	parietal	SCAN
rs957828	BCL10	cis	cerebellum	SCAN
rs957828	ZNF790	trans	cerebellum	SCAN
rs957828	LOC339524	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84536600-84542400	Weak transcription	Fetal Lung	lung
2	chr1:84538000-84542000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:84538400-84542400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:84538400-84542800	Weak transcription	HSMM	muscle
5	chr1:84538600-84542000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:84538600-84542400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:84538600-84542400	Weak transcription	Osteobl	bone
8	chr1:84538800-84542200	Weak transcription	Fetal Brain Male	brain
9	chr1:84539200-84542000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:84539200-84542400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:84540200-84542400	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:84541000-84542000	Weak transcription	A549	lung
13	chr1:84541000-84542000	Enhancers	K562	blood
14	chr1:84541000-84542400	Enhancers	HepG2	liver
15	chr1:84541200-84541800	Enhancers	Brain Cingulate Gyrus	brain
16	chr1:84541200-84542400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:84541200-84542400	Enhancers	Brain Hippocampus Middle	brain
18	chr1:84541200-84542400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:84541200-84542400	Enhancers	Dnd41	blood
20	chr1:84541400-84542000	Weak transcription	Liver	Liver
21	chr1:84541400-84542400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:84541400-84542400	Weak transcription	Brain Anterior Caudate	brain
23	chr1:84541400-84542600	Weak transcription	Brain Substantia Nigra	brain
24	chr1:84541600-84542000	Weak transcription	GM12878-XiMat	blood

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