Variant report

Variant	rs2294706
Chromosome Location	chr6:163942162-163942163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163941356..163943183-chr6:163944716..163947112,2	K562	blood:
2	chr6:163919801..163922242-chr6:163941031..163943536,2	K562	blood:
3	chr6:163936784..163940539-chr6:163940693..163944816,5	K562	blood:
4	chr6:163932152..163934277-chr6:163941799..163943537,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1047935	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11962088	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs13199835	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13202282	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16895015	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1737328	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs17591955	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2143358	0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2294698	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2294703	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2294709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35442073	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3756879	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs3763197	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4263561	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs4709716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4709717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4709718	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4709720	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4709722	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6455897	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs6931903	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6939218	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs715020	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs724826	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758706	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7772756	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs9346960	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9347760	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9364688	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9364689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9364691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9364692	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1019551	chr6:163842358-163965216	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1017495	chr6:163856399-163981095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv2763608	chr6:163920117-163943429	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1027863	chr6:163934616-163965216	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2294706	LOC285796	cis	lymphoblastoid	seeQTL
rs2294706	SESTD1	trans	cerebellum	SCAN
rs2294706	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163926600-163946200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:163926600-163946600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:163926600-163991800	Weak transcription	Esophagus	oesophagus
4	chr6:163927200-163951600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:163928200-163951600	Weak transcription	Spleen	Spleen
6	chr6:163928800-163942800	Weak transcription	HSMM	muscle
7	chr6:163928800-163944000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:163928800-163946600	Weak transcription	HUVEC	blood vessel
9	chr6:163929000-163947200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:163929200-163946600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:163929200-163946800	Weak transcription	HMEC	breast
12	chr6:163929400-163943800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr6:163929400-163946600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:163929600-163947200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:163929600-163950800	Weak transcription	Fetal Lung	lung
16	chr6:163929600-163951600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:163929800-163957000	Weak transcription	Primary B cells from cord blood	blood
18	chr6:163930600-163943600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:163930600-163950200	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:163934200-163946600	Weak transcription	NHEK	skin
21	chr6:163934200-163949200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:163935200-163943800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:163935200-163946000	Weak transcription	A549	lung
24	chr6:163935200-163946400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:163935200-163946800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:163935200-163947400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:163935200-163950600	Weak transcription	Ovary	ovary
28	chr6:163935200-163952200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:163935200-163958800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:163935200-163959400	Weak transcription	Lung	lung
31	chr6:163935400-163943000	Weak transcription	Liver	Liver
32	chr6:163935400-163951600	Weak transcription	Pancreas	Pancrea
33	chr6:163935800-163943000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:163936800-163947200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:163936800-163953600	Enhancers	Brain Hippocampus Middle	brain
36	chr6:163936800-163957400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr6:163937800-163943800	Enhancers	Brain Substantia Nigra	brain
38	chr6:163938000-163942400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr6:163938000-163943800	Enhancers	Brain Cingulate Gyrus	brain
40	chr6:163938200-163942600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:163938200-163951000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:163938400-163946200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:163938600-163946200	Weak transcription	Right Atrium	heart
44	chr6:163939400-163943800	Weak transcription	K562	blood
45	chr6:163939600-163944200	Enhancers	Adipose Nuclei	Adipose
46	chr6:163939800-163956200	Enhancers	Brain Anterior Caudate	brain
47	chr6:163940000-163942200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr6:163940000-163945200	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr6:163940000-163945400	Enhancers	Brain Angular Gyrus	brain
50	chr6:163940200-163946400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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