Variant report

Variant	rs11774499
Chromosome Location	chr8:87547273-87547274
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	chr8:87520330..87522050-chr8:87545788..87547442,3	MCF-7	breast:
2	chr8:87526728..87528927-chr8:87546048..87547897,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085719	Chromatin interaction
ENSG00000176623	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10086188	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10089169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10089253	0.84[ASN][1000 genomes]
rs10090898	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10090963	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10092168	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10094332	1.00[ASN][1000 genomes]
rs10095589	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10097866	0.84[ASN][1000 genomes]
rs10098365	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10100182	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10100247	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10100254	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10100368	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10100698	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10106390	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10107117	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10107571	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10108586	0.84[ASN][1000 genomes]
rs10110096	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10481195	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10956820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10956822	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10956871	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11776698	0.84[ASN][1000 genomes]
rs11783382	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11984519	0.90[ASN][1000 genomes]
rs11986423	0.85[GIH][hapmap];1.00[ASN][1000 genomes]
rs11994508	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11997927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11998558	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12155981	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs16915375	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16915389	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17681534	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28397606	0.90[ASN][1000 genomes]
rs28416254	0.90[ASN][1000 genomes]
rs28438974	1.00[ASN][1000 genomes]
rs28514445	1.00[ASN][1000 genomes]
rs28540009	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613262	1.00[ASN][1000 genomes]
rs28687116	1.00[ASN][1000 genomes]
rs3087641	0.87[CHD][hapmap];0.82[GIH][hapmap];0.90[ASN][1000 genomes]
rs4440616	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs57638937	0.82[ASN][1000 genomes]
rs58837061	0.84[ASN][1000 genomes]
rs6651177	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6651268	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67332431	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6980476	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6992624	0.90[ASN][1000 genomes]
rs7015772	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7018083	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72690416	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72690443	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690445	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690447	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690455	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690457	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690474	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73688856	0.84[ASN][1000 genomes]
rs73688857	0.88[ASN][1000 genomes]
rs73688858	0.88[ASN][1000 genomes]
rs73688859	0.81[ASN][1000 genomes]
rs73688862	0.88[ASN][1000 genomes]
rs7818436	0.90[ASN][1000 genomes]
rs7823951	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7824873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7833201	0.97[ASN][1000 genomes]
rs7843399	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7844014	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9297913	0.90[ASN][1000 genomes]
rs9650128	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650129	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
2	nsv1023510	chr8:87429001-87874948	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv933966	chr8:87454655-87591558	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11774499	CPNE3	cis	cerebellum	SCAN
rs11774499	CPNE3	cis	parietal	SCAN
rs11774499	FAM82B	cis	cerebellum	SCAN
rs11774499	FAM82B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87527400-87568400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:87527600-87550200	Weak transcription	Aorta	Aorta
3	chr8:87527600-87562000	Weak transcription	Pancreas	Pancrea
4	chr8:87527600-87568200	Weak transcription	Gastric	stomach
5	chr8:87527600-87584000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr8:87527800-87547400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr8:87527800-87560000	Weak transcription	HSMMtube	muscle
8	chr8:87528000-87550800	Weak transcription	Psoas Muscle	Psoas
9	chr8:87528000-87551400	Weak transcription	Right Ventricle	heart
10	chr8:87528000-87563800	Weak transcription	Hela-S3	cervix
11	chr8:87528000-87573600	Weak transcription	Stomach Mucosa	stomach
12	chr8:87528200-87572000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr8:87528400-87550400	Weak transcription	HepG2	liver
14	chr8:87528400-87560400	Weak transcription	Thymus	Thymus
15	chr8:87528600-87548600	Weak transcription	Fetal Brain Male	brain
16	chr8:87528600-87557200	Weak transcription	Small Intestine	intestine
17	chr8:87528600-87566000	Weak transcription	Spleen	Spleen
18	chr8:87529400-87549000	Weak transcription	Brain Substantia Nigra	brain
19	chr8:87535600-87547800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr8:87535800-87548800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr8:87536000-87559400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr8:87536200-87550000	Weak transcription	NH-A	brain
23	chr8:87536200-87550400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr8:87536400-87548400	Weak transcription	HUVEC	blood vessel
25	chr8:87536400-87550600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr8:87536600-87556600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr8:87539400-87551800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr8:87539400-87552000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr8:87539400-87554000	Strong transcription	Fetal Intestine Large	intestine
30	chr8:87539600-87550000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr8:87539600-87560200	Weak transcription	Lung	lung
32	chr8:87540400-87554800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr8:87541200-87554800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr8:87541400-87547400	Strong transcription	Adipose Nuclei	Adipose
35	chr8:87541400-87554800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr8:87541600-87553000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr8:87541600-87563800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr8:87541600-87570600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr8:87542000-87548400	Weak transcription	HSMM	muscle
40	chr8:87542000-87558800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr8:87542400-87553000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr8:87542600-87550200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr8:87542600-87554400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr8:87543000-87553600	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr8:87543200-87555000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr8:87543200-87571200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr8:87543200-87572600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr8:87543400-87547400	Strong transcription	Osteobl	bone
49	chr8:87543400-87547600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr8:87543400-87548000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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