Variant report

Variant	rs12677183
Chromosome Location	chr8:99559950-99559951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10096329	0.81[JPT][hapmap]
rs10755896	0.85[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10755897	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10955178	0.82[JPT][hapmap]
rs10955186	1.00[ASW][hapmap];0.87[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10955187	1.00[ASW][hapmap];0.87[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10955188	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10955189	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10955190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11774463	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs11775055	0.81[AMR][1000 genomes]
rs11780292	0.82[ASN][1000 genomes]
rs11780369	0.82[ASN][1000 genomes]
rs11780500	0.86[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs11785245	0.82[JPT][hapmap]
rs12542069	1.00[ASW][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12542649	0.86[ASN][1000 genomes]
rs12542758	0.82[CHB][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12547297	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs12549803	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[ASN][1000 genomes]
rs12550012	0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12550783	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12675964	0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12679268	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12680195	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs12680490	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12680602	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13257475	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs13258214	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13269932	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13271844	0.89[ASN][1000 genomes]
rs13275915	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs16897076	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs34114299	0.85[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34477118	0.88[ASN][1000 genomes]
rs34855977	0.89[ASN][1000 genomes]
rs35447893	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4131873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4279561	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4442112	0.85[GIH][hapmap]
rs4509292	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4517094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4541872	0.81[ASN][1000 genomes]
rs4549741	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4612309	0.88[ASN][1000 genomes]
rs4734410	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4735568	1.00[ASW][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4735569	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4735570	1.00[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[LWK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.82[ASN][1000 genomes]
rs4735571	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4735574	0.86[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs62532565	0.81[ASN][1000 genomes]
rs62535381	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62535404	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62535408	0.91[ASN][1000 genomes]
rs62535410	0.90[ASN][1000 genomes]
rs62535412	0.89[ASN][1000 genomes]
rs6651182	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6988087	0.93[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs6992925	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7016626	0.83[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs72666669	0.83[ASN][1000 genomes]
rs7816638	0.87[ASN][1000 genomes]
rs7818010	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7818828	0.95[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs7838239	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9656842	0.85[ASW][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12677183	NCALD	cis	cerebellum	SCAN
rs12677183	OSR2	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99525800-99576400	Weak transcription	Pancreas	Pancrea
2	chr8:99531000-99569600	Weak transcription	HMEC	breast
3	chr8:99531200-99561800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr8:99531400-99586400	Weak transcription	HSMM	muscle
5	chr8:99531600-99561800	Weak transcription	Esophagus	oesophagus
6	chr8:99533400-99566400	Weak transcription	NHLF	lung
7	chr8:99534600-99567200	Weak transcription	A549	lung
8	chr8:99535400-99571600	Weak transcription	Gastric	stomach
9	chr8:99543000-99566800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr8:99544000-99560800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr8:99544000-99566800	Weak transcription	Brain Substantia Nigra	brain
12	chr8:99544600-99560000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr8:99544600-99587000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr8:99546000-99571600	Weak transcription	Fetal Intestine Small	intestine
15	chr8:99546600-99576400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr8:99548400-99560800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr8:99548600-99569800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr8:99548800-99563400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr8:99549800-99568200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr8:99550800-99560200	Weak transcription	Right Ventricle	heart
21	chr8:99551200-99560400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:99551200-99561800	Weak transcription	Brain Angular Gyrus	brain
23	chr8:99551400-99566000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr8:99551800-99562000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr8:99552000-99572600	Weak transcription	Brain Hippocampus Middle	brain
26	chr8:99553400-99560800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr8:99553400-99569600	Weak transcription	Fetal Lung	lung
28	chr8:99553400-99586000	Weak transcription	Ovary	ovary
29	chr8:99553600-99589600	Weak transcription	Fetal Stomach	stomach
30	chr8:99553800-99561800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr8:99553800-99566800	Weak transcription	Adipose Nuclei	Adipose
32	chr8:99554200-99567800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr8:99554800-99572800	Weak transcription	Dnd41	blood
34	chr8:99554800-99593200	Weak transcription	K562	blood
35	chr8:99555400-99564000	Weak transcription	Primary T cells from cord blood	blood
36	chr8:99556000-99560400	Strong transcription	Left Ventricle	heart
37	chr8:99556000-99560800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr8:99556000-99571600	Weak transcription	Fetal Intestine Large	intestine
39	chr8:99556200-99560400	Weak transcription	Lung	lung
40	chr8:99556200-99606200	Weak transcription	Psoas Muscle	Psoas
41	chr8:99557000-99560200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr8:99557000-99560400	Strong transcription	NHEK	skin
43	chr8:99557200-99560400	Strong transcription	Placenta	Placenta
44	chr8:99557800-99560400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr8:99557800-99581400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr8:99558000-99560600	Weak transcription	Colonic Mucosa	Colon
47	chr8:99558600-99560000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr8:99558600-99560400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr8:99558800-99560000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr8:99558800-99560000	Strong transcription	HSMMtube	muscle

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