Variant report

Variant	rs2294709
Chromosome Location	chr6:163907241-163907242
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163906959..163909795-chr6:163909978..163912213,2	K562	blood:
2	chr6:163907164..163909341-chr6:163918489..163921263,2	K562	blood:
3	chr6:163906185..163908152-chr6:163909276..163911909,3	MCF-7	breast:
4	chr6:163906576..163909444-chr6:163912230..163915189,4	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1047935	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11962088	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs13199835	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13202282	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16895015	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
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]
rs2294698	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2294703	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2294706	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]
rs2294707	0.86[ASN][1000 genomes]
rs35442073	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[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];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs4708995	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4709716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4709717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4709718	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4709720	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4709722	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[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];0.86[ASN][1000 genomes]
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];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs724826	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73015387	0.82[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];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9347760	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9364688	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9364689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9364691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9364692	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1797109	chr6:163834147-163908115	Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv523664	chr6:163858237-163907885	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2294709	SESTD1	trans	cerebellum	SCAN
rs2294709	QKI	Cis_1M	lymphoblastoid	RTeQTL
rs2294709	LOC285796	cis	lymphoblastoid	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163878800-163910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:163881800-163910800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:163888400-163908200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:163890800-163911400	Weak transcription	Osteobl	bone
5	chr6:163891400-163910200	Weak transcription	HUVEC	blood vessel
6	chr6:163892200-163911400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:163892600-163910400	Weak transcription	HMEC	breast
8	chr6:163893000-163912800	Weak transcription	Fetal Brain Male	brain
9	chr6:163893400-163912000	Weak transcription	Fetal Lung	lung
10	chr6:163893600-163910200	Weak transcription	HSMMtube	muscle
11	chr6:163896600-163910800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr6:163898000-163907800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:163898400-163908200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:163898400-163909000	Weak transcription	Fetal Brain Female	brain
15	chr6:163898400-163911600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:163898400-163926000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:163898600-163907800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:163898800-163908000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:163899200-163910200	Weak transcription	Hela-S3	cervix
20	chr6:163899600-163910400	Weak transcription	NHLF	lung
21	chr6:163899800-163911000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:163899800-163911600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:163900000-163908000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:163901000-163910400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:163901200-163907800	Weak transcription	Brain Germinal Matrix	brain
26	chr6:163901200-163908200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:163901400-163908600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr6:163901600-163910200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:163901600-163910200	Weak transcription	NH-A	brain
30	chr6:163901600-163910400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:163902200-163913600	Enhancers	Brain Anterior Caudate	brain
32	chr6:163902400-163908400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:163902600-163909400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:163902600-163921800	Weak transcription	HepG2	liver
35	chr6:163902800-163908000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr6:163902800-163912200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:163903000-163908000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:163903000-163909200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr6:163903000-163909200	Weak transcription	HSMM	muscle
40	chr6:163903000-163915000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:163903000-163924200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:163903200-163910600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:163903400-163910400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:163903600-163911400	Weak transcription	Fetal Thymus	thymus
45	chr6:163903600-163926000	Weak transcription	Lung	lung
46	chr6:163903800-163912200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:163904000-163908000	Weak transcription	GM12878-XiMat	blood
48	chr6:163904000-163908200	Weak transcription	Right Atrium	heart
49	chr6:163904000-163908400	Weak transcription	Primary B cells from cord blood	blood
50	chr6:163904000-163917400	Weak transcription	Fetal Muscle Leg	muscle

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