Variant report

Variant	rs2977008
Chromosome Location	chr8:52308575-52308576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10091279	0.80[YRI][hapmap]
rs10096044	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10101803	0.80[YRI][hapmap]
rs10104348	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1017354	0.80[YRI][hapmap]
rs10958261	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs1219677	0.80[YRI][hapmap]
rs1219680	0.82[ASW][hapmap];0.87[LWK][hapmap];0.80[YRI][hapmap]
rs12550267	0.81[AFR][1000 genomes]
rs12550699	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13282560	0.86[AMR][1000 genomes]
rs1367820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1431620	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs1560511	0.86[AMR][1000 genomes]
rs1811360	0.84[EUR][1000 genomes]
rs1975113	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2082279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915487	0.87[AFR][1000 genomes]
rs2915488	0.87[AFR][1000 genomes]
rs2915489	0.84[YRI][hapmap]
rs2915492	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2915493	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2915495	1.00[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2915502	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2915504	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2915505	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2976994	0.83[LWK][hapmap]
rs2976998	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2976999	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2977000	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2977001	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2977002	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2977003	0.91[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2977004	0.81[EUR][1000 genomes]
rs2977005	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2977010	1.00[ASW][hapmap];0.82[CEU][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2977012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2977015	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2977020	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3097700	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3097702	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs4471026	0.81[AFR][1000 genomes]
rs4873548	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60579236	0.84[AFR][1000 genomes]
rs6996951	0.80[YRI][hapmap]
rs7004184	0.86[AMR][1000 genomes]
rs766788	0.80[YRI][hapmap]
rs766790	0.80[YRI][hapmap]
rs9298444	0.82[ASW][hapmap];0.85[LWK][hapmap];0.80[YRI][hapmap]
rs961353	0.91[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs972026	0.91[ASW][hapmap];0.92[LWK][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932026	chr8:51858658-52758574	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv948338	chr8:52060314-52368754	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv890895	chr8:52190571-52615191	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2977008	RB1CC1	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52302800-52310800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr8:52303000-52310800	Weak transcription	Fetal Stomach	stomach
3	chr8:52305800-52309800	Enhancers	Primary B cells from peripheral blood	blood
4	chr8:52307000-52308600	Enhancers	HMEC	breast
5	chr8:52307000-52308800	Enhancers	Osteobl	bone
6	chr8:52307000-52309000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr8:52307000-52309400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr8:52307000-52309600	Enhancers	NH-A	brain
9	chr8:52307000-52312400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr8:52307200-52308800	Enhancers	Left Ventricle	heart
11	chr8:52307200-52309000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr8:52307200-52309000	Enhancers	Right Atrium	heart
13	chr8:52307400-52308800	Enhancers	NHLF	lung
14	chr8:52307400-52309000	Enhancers	GM12878-XiMat	blood
15	chr8:52307400-52310000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr8:52307600-52310600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr8:52307600-52310800	Weak transcription	Spleen	Spleen
18	chr8:52307600-52320600	Weak transcription	Right Ventricle	heart
19	chr8:52307800-52308600	Enhancers	Fetal Lung	lung
20	chr8:52308000-52310800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr8:52308200-52308600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr8:52308200-52309000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr8:52308200-52309000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr8:52308200-52309000	Flanking Active TSS	NHDF-Ad	bronchial
25	chr8:52308400-52308600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr8:52308400-52308800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr8:52308400-52308800	Enhancers	A549	lung
28	chr8:52308400-52309000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr8:52308400-52309000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr8:52308400-52309000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr8:52308400-52309000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr8:52308400-52309200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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