Variant report

Variant	rs2607659
Chromosome Location	chr8:103240003-103240004
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103239162..103241164-chr8:103243127..103246074,2	K562	blood:
2	chr8:103229075..103231753-chr8:103237242..103240149,2	K562	blood:
3	chr8:103224036..103225570-chr8:103238555..103240189,2	K562	blood:
4	chr8:103238918..103240995-chr8:103242872..103245266,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000048392	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12114277	0.83[GIH][hapmap];0.83[MEX][hapmap]
rs2512409	0.81[GIH][hapmap]
rs2607657	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607662	0.84[CHD][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs2853228	0.82[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2853229	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2853233	0.88[CHD][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs2853238	0.83[GIH][hapmap]
rs3931977	0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs4102400	0.86[CHB][hapmap];0.87[MEX][hapmap]
rs6468819	0.82[ASN][1000 genomes]
rs6980902	0.83[CEU][hapmap];0.90[CHB][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020359	chr8:103109921-103318415	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1021459	chr8:103163436-103401754	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv539701	chr8:103163436-103401754	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1018990	chr8:103207922-103357742	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539702	chr8:103207922-103357742	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1028890	chr8:103207922-103401754	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv891242	chr8:103210971-103282418	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv891243	chr8:103219629-103292724	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	esv1797821	chr8:103234077-103241531	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2607659	KCNS2	cis	cerebellum	SCAN
rs2607659	PABPC1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103209800-103244800	Weak transcription	Stomach Mucosa	stomach
2	chr8:103215600-103248400	Weak transcription	Psoas Muscle	Psoas
3	chr8:103216200-103247400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr8:103216400-103245200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr8:103216400-103246600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr8:103217000-103248400	Weak transcription	Small Intestine	intestine
7	chr8:103217200-103240200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr8:103217200-103240200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr8:103217800-103246400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr8:103218000-103246200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr8:103218600-103244200	Weak transcription	Fetal Heart	heart
12	chr8:103219200-103247600	Weak transcription	Fetal Brain Male	brain
13	chr8:103220400-103248800	Weak transcription	Hela-S3	cervix
14	chr8:103222600-103246000	Strong transcription	Osteobl	bone
15	chr8:103227600-103246800	Strong transcription	Primary B cells from cord blood	blood
16	chr8:103228000-103242200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr8:103229600-103240200	Strong transcription	Placenta	Placenta
18	chr8:103229600-103246800	Strong transcription	Primary hematopoietic stem cells	blood
19	chr8:103229800-103245000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr8:103230000-103242200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr8:103231400-103240600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr8:103231600-103240400	Weak transcription	Gastric	stomach
23	chr8:103231600-103249800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr8:103232000-103240200	Weak transcription	Colonic Mucosa	Colon
25	chr8:103232000-103242600	Weak transcription	HepG2	liver
26	chr8:103234600-103240200	Weak transcription	A549	lung
27	chr8:103234600-103250000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr8:103234800-103240200	Weak transcription	Brain Angular Gyrus	brain
29	chr8:103234800-103240400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr8:103234800-103240600	Weak transcription	Esophagus	oesophagus
31	chr8:103234800-103242400	Weak transcription	NHLF	lung
32	chr8:103234800-103242800	Weak transcription	Brain Germinal Matrix	brain
33	chr8:103236600-103245800	Strong transcription	HSMMtube	muscle
34	chr8:103237200-103248400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr8:103237400-103240200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr8:103237400-103242200	Weak transcription	NHDF-Ad	bronchial
37	chr8:103237400-103245400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr8:103237600-103240600	Weak transcription	HUVEC	blood vessel
39	chr8:103238000-103240200	Weak transcription	NHEK	skin
40	chr8:103238200-103248800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr8:103238400-103240200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr8:103238400-103248200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr8:103238400-103248800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr8:103239000-103240200	Strong transcription	Lung	lung
45	chr8:103239200-103240800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
46	chr8:103239200-103244000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr8:103239400-103240200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr8:103239400-103240200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr8:103239400-103240600	Strong transcription	Fetal Brain Female	brain
50	chr8:103239400-103241800	Strong transcription	H1 Cell Line	embryonic stem cell

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