Variant report

Variant	rs2853229
Chromosome Location	chr8:103247134-103247135
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12114277	0.84[GIH][hapmap];0.87[MEX][hapmap]
rs2512409	0.82[GIH][hapmap]
rs2607657	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607658	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2607659	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]
rs2607662	0.84[CHD][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs2853228	0.82[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2853233	0.88[CHD][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.84[ASN][1000 genomes]
rs2853238	0.84[GIH][hapmap]
rs3931977	0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs4102400	0.86[CHB][hapmap];0.92[MEX][hapmap]
rs6468819	0.80[ASN][1000 genomes]
rs6980902	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs7827839	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2853229	CTHRC1	cis	parietal	SCAN
rs2853229	KCNS2	cis	cerebellum	SCAN
rs2853229	PABPC1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103215600-103248400	Weak transcription	Psoas Muscle	Psoas
2	chr8:103216200-103247400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr8:103217000-103248400	Weak transcription	Small Intestine	intestine
4	chr8:103219200-103247600	Weak transcription	Fetal Brain Male	brain
5	chr8:103220400-103248800	Weak transcription	Hela-S3	cervix
6	chr8:103231600-103249800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr8:103234600-103250000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr8:103237200-103248400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr8:103238200-103248800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr8:103238400-103248200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr8:103238400-103248800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr8:103240800-103247600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr8:103240800-103247600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr8:103240800-103248800	Weak transcription	Pancreas	Pancrea
15	chr8:103240800-103249000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr8:103240800-103249000	Weak transcription	Gastric	stomach
17	chr8:103241000-103247200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr8:103241000-103248000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr8:103241000-103248200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr8:103241000-103248200	Weak transcription	Aorta	Aorta
21	chr8:103241000-103248400	Weak transcription	Lung	lung
22	chr8:103241000-103248400	Weak transcription	Thymus	Thymus
23	chr8:103241000-103248600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr8:103241000-103248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr8:103241000-103248800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr8:103241000-103249000	Weak transcription	Right Ventricle	heart
27	chr8:103241000-103249200	Weak transcription	Colonic Mucosa	Colon
28	chr8:103241000-103250400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr8:103241000-103250400	Weak transcription	Esophagus	oesophagus
30	chr8:103241200-103248600	Weak transcription	Ovary	ovary
31	chr8:103241200-103249000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr8:103241200-103249000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr8:103241400-103248400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr8:103241400-103249600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr8:103241400-103250600	Weak transcription	Spleen	Spleen
36	chr8:103242000-103249400	Weak transcription	Fetal Stomach	stomach
37	chr8:103242400-103248400	Strong transcription	HSMM	muscle
38	chr8:103242600-103249200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr8:103243200-103248600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr8:103243400-103248600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr8:103243400-103249800	Weak transcription	Fetal Kidney	kidney
42	chr8:103243600-103248000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr8:103243600-103248200	Weak transcription	Brain Substantia Nigra	brain
44	chr8:103243600-103248400	Weak transcription	K562	blood
45	chr8:103243600-103248600	Weak transcription	Brain Hippocampus Middle	brain
46	chr8:103243600-103248600	Weak transcription	A549	lung
47	chr8:103243600-103248800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr8:103243600-103249200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr8:103243600-103250200	Weak transcription	Placenta	Placenta
50	chr8:103243800-103247400	Weak transcription	Colon Smooth Muscle	Colon

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