Variant report

Variant	rs2812683
Chromosome Location	chr6:80323834-80323835
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:80318365..80321776-chr6:80322794..80325239,3	K562	blood:
2	chr6:80316501..80318082-chr6:80322161..80324470,2	K562	blood:
3	chr6:80314864..80317185-chr6:80322166..80324307,2	MCF-7	breast:
4	chr6:80314232..80316495-chr6:80323801..80327560,3	K562	blood:
5	chr6:80318741..80320286-chr6:80322794..80325541,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10081125	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12208969	0.85[TSI][hapmap]
rs2245410	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[ASN][1000 genomes]
rs2245419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2655697	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812679	0.85[ASN][1000 genomes]
rs2812682	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814379	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2814380	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2814383	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2814384	0.86[ASN][1000 genomes]
rs56268574	0.84[ASN][1000 genomes]
rs62413410	0.83[ASN][1000 genomes]
rs9294152	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1018318	chr6:80241029-80465282	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv886304	chr6:80294265-80355973	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2812683	TTK	cis	parietal	SCAN
rs2812683	HMGN3	cis	cerebellum	SCAN
rs2812683	SH3BGRL2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80298600-80324200	Weak transcription	Right Ventricle	heart
2	chr6:80311000-80324400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr6:80311200-80324400	Weak transcription	Pancreas	Pancrea
4	chr6:80315000-80340600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:80317400-80324400	Weak transcription	Left Ventricle	heart
6	chr6:80318000-80340200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:80319200-80324400	Weak transcription	Fetal Heart	heart
8	chr6:80319400-80328000	Weak transcription	Esophagus	oesophagus
9	chr6:80320600-80324000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:80320600-80324200	Weak transcription	Fetal Intestine Large	intestine
11	chr6:80320600-80324200	Weak transcription	Lung	lung
12	chr6:80320800-80338600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:80321600-80325200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:80322200-80325000	Enhancers	Stomach Mucosa	stomach
15	chr6:80322400-80330600	Enhancers	HepG2	liver
16	chr6:80322600-80324400	Enhancers	Gastric	stomach
17	chr6:80322600-80326400	Enhancers	Placenta	Placenta
18	chr6:80322600-80340000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:80322800-80340400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:80323000-80324000	Weak transcription	Fetal Intestine Small	intestine
21	chr6:80323200-80324600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:80323200-80330400	Enhancers	Liver	Liver
23	chr6:80323400-80325400	Enhancers	GM12878-XiMat	blood
24	chr6:80323600-80324000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:80323600-80325000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:80323800-80325400	Enhancers	K562	blood

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