Variant report

Variant	rs16897076
Chromosome Location	chr8:99558354-99558355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:99557700..99559329-chr8:100024185..100025880,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253948	Chromatin interaction
ENSG00000132549	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10441501	0.82[JPT][hapmap]
rs10755896	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs10755897	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs10955178	1.00[JPT][hapmap]
rs10955179	0.86[JPT][hapmap]
rs10955186	0.86[GIH][hapmap]
rs10955187	0.86[GIH][hapmap]
rs10955190	0.95[CHB][hapmap]
rs11774463	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs11985382	0.82[JPT][hapmap]
rs12056323	0.82[JPT][hapmap]
rs12542022	0.82[JPT][hapmap]
rs12547297	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs12549803	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs12550012	0.82[CHD][hapmap]
rs12550783	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12675964	0.80[CHD][hapmap]
rs12677183	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs12679268	0.86[ASN][1000 genomes]
rs12680195	0.91[CHB][hapmap];0.89[CHD][hapmap]
rs13257475	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13269932	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs13270534	0.82[JPT][hapmap]
rs13271844	0.82[ASN][1000 genomes]
rs13275915	0.95[CHB][hapmap];0.91[CHD][hapmap]
rs16897061	0.82[JPT][hapmap];0.83[MEX][hapmap]
rs1893884	0.82[JPT][hapmap]
rs34114299	0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs34477118	0.81[ASN][1000 genomes]
rs34855977	0.82[ASN][1000 genomes]
rs4130753	0.82[JPT][hapmap]
rs4131873	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.81[LWK][hapmap]
rs4279561	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap]
rs4370499	0.82[JPT][hapmap]
rs4388428	0.82[JPT][hapmap]
rs4442112	0.81[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4509292	0.91[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4517094	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs4549741	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap]
rs4612309	0.81[ASN][1000 genomes]
rs4734410	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4735564	0.82[JPT][hapmap]
rs4735569	0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4735570	0.86[CHB][hapmap]
rs4735574	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs62535404	0.82[ASN][1000 genomes]
rs62535408	0.84[ASN][1000 genomes]
rs62535410	0.83[ASN][1000 genomes]
rs62535412	0.82[ASN][1000 genomes]
rs6651182	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs6992925	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs7011763	0.82[JPT][hapmap]
rs7016626	0.83[CHB][hapmap];0.82[JPT][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7816638	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7818010	0.82[CHB][hapmap]
rs7838239	0.82[CHB][hapmap]

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	nsv1027362	chr8:99469281-99715845	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv539689	chr8:99469281-99715845	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv891218	chr8:99507313-99906221	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv891219	chr8:99526819-99643487	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv611808	chr8:99544765-99591736	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv1030498	chr8:99545493-99607093	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16897076	OSR2	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99500400-99558800	Weak transcription	Aorta	Aorta
2	chr8:99525800-99576400	Weak transcription	Pancreas	Pancrea
3	chr8:99531000-99569600	Weak transcription	HMEC	breast
4	chr8:99531200-99561800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr8:99531400-99586400	Weak transcription	HSMM	muscle
6	chr8:99531600-99561800	Weak transcription	Esophagus	oesophagus
7	chr8:99533400-99566400	Weak transcription	NHLF	lung
8	chr8:99534600-99567200	Weak transcription	A549	lung
9	chr8:99535400-99571600	Weak transcription	Gastric	stomach
10	chr8:99543000-99566800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr8:99544000-99559000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr8:99544000-99560800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr8:99544000-99566800	Weak transcription	Brain Substantia Nigra	brain
14	chr8:99544200-99558800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr8:99544200-99559400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr8:99544600-99560000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr8:99544600-99587000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr8:99546000-99571600	Weak transcription	Fetal Intestine Small	intestine
19	chr8:99546600-99576400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr8:99548400-99560800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr8:99548600-99558800	Weak transcription	HSMMtube	muscle
22	chr8:99548600-99569800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:99548800-99563400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr8:99549800-99568200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr8:99550800-99560200	Weak transcription	Right Ventricle	heart
26	chr8:99551200-99558800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr8:99551200-99559400	Weak transcription	Small Intestine	intestine
28	chr8:99551200-99560400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr8:99551200-99561800	Weak transcription	Brain Angular Gyrus	brain
30	chr8:99551400-99566000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr8:99551800-99562000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr8:99552000-99572600	Weak transcription	Brain Hippocampus Middle	brain
33	chr8:99552600-99559800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr8:99552800-99559000	Weak transcription	GM12878-XiMat	blood
35	chr8:99553000-99559600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr8:99553200-99558600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr8:99553400-99559400	Weak transcription	HepG2	liver
38	chr8:99553400-99560800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr8:99553400-99569600	Weak transcription	Fetal Lung	lung
40	chr8:99553400-99586000	Weak transcription	Ovary	ovary
41	chr8:99553600-99589600	Weak transcription	Fetal Stomach	stomach
42	chr8:99553800-99558600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr8:99553800-99558800	Weak transcription	Liver	Liver
44	chr8:99553800-99561800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr8:99553800-99566800	Weak transcription	Adipose Nuclei	Adipose
46	chr8:99554200-99567800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr8:99554800-99558800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr8:99554800-99572800	Weak transcription	Dnd41	blood
49	chr8:99554800-99593200	Weak transcription	K562	blood
50	chr8:99555000-99558800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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