Variant report

Variant	rs11259742
Chromosome Location	chr10:5647078-5647079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr10:5639024..5641662-chr10:5646030..5647714,3	K562	blood:
2	chr10:5589894..5591628-chr10:5645906..5647922,4	MCF-7	breast:
3	chr10:5529023..5530899-chr10:5646975..5649867,2	MCF-7	breast:
4	chr10:5622553..5625678-chr10:5643794..5647662,4	MCF-7	breast:
5	chr10:5486648..5491055-chr10:5645215..5653179,9	MCF-7	breast:
6	chr10:5644299..5647133-chr10:5657703..5660499,2	K562	blood:
7	chr10:5589034..5590699-chr10:5646988..5649600,2	MCF-7	breast:
8	chr10:5533616..5541618-chr10:5644676..5651501,11	MCF-7	breast:
9	chr10:5625746..5627987-chr10:5645084..5647138,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000178372	Chromatin interaction
ENSG00000228951	Chromatin interaction
ENSG00000173848	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10904531	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11255051	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11255916	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11258033	0.91[MEX][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap]
rs11259544	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11259582	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11259704	0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11818357	0.81[EUR][1000 genomes]
rs12260316	0.81[EUR][1000 genomes]
rs1544216	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2380196	0.83[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.86[ASN][1000 genomes]
rs2380197	0.86[ASN][1000 genomes]
rs2386663	0.82[GIH][hapmap]
rs4747358	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56226546	0.81[EUR][1000 genomes]
rs57893347	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61832660	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61832676	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6601981	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs7093321	0.81[EUR][1000 genomes]
rs72781996	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7350438	0.96[MEX][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap]
rs7896078	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7924096	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv831774	chr10:5463556-5657421	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv894798	chr10:5503610-5670275	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv523491	chr10:5542109-5720067	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	esv2757364	chr10:5557024-5720512	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1036798	chr10:5637870-5652754	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1040932	chr10:5637870-5665774	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv466718	chr10:5639907-5657527	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv549890	chr10:5639907-5657527	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv2753567	chr10:5641348-5652237	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv894806	chr10:5643511-5670275	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1054888	chr10:5645033-5694612	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv466719	chr10:5645895-5662915	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv549891	chr10:5645895-5662915	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv519582	chr10:5646103-5720067	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11259742	DOCK6	trans	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5634800-5651200	Weak transcription	Pancreas	Pancrea
2	chr10:5639800-5650200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr10:5639800-5651600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr10:5642600-5651000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr10:5643600-5648400	Weak transcription	Esophagus	oesophagus
6	chr10:5644000-5648600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:5644200-5650600	Weak transcription	Liver	Liver
8	chr10:5645000-5651800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr10:5645400-5647800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:5645600-5647600	Weak transcription	Fetal Intestine Small	intestine
11	chr10:5645600-5648400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:5645600-5650400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:5646000-5650200	Weak transcription	HMEC	breast
14	chr10:5646400-5647800	Enhancers	Fetal Thymus	thymus
15	chr10:5646400-5648800	Enhancers	HepG2	liver
16	chr10:5647000-5647200	Enhancers	Adipose Nuclei	Adipose
17	chr10:5647000-5647400	Enhancers	Fetal Muscle Trunk	muscle
18	chr10:5647000-5649200	Enhancers	Fetal Muscle Leg	muscle

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