Variant report

Variant	rs9326863
Chromosome Location	chr5:112056360-112056361
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112053504..112055952-chr5:112056185..112057959,2	MCF-7	breast:
2	chr5:112053751..112057397-chr5:112071808..112074498,3	K562	blood:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10051624	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10071425	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10072068	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10073398	0.87[EUR][1000 genomes]
rs10075281	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10075323	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10075377	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10076641	0.92[EUR][1000 genomes]
rs10213844	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10477483	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1093611	0.81[CHD][hapmap]
rs11241182	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11241183	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11241184	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11241185	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs11749632	0.88[EUR][1000 genomes]
rs11749701	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11954856	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs12332692	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12513787	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12513804	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs12518091	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12658609	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12659119	0.88[EUR][1000 genomes]
rs12719151	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs13156251	0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13173990	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs1441367	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1465910	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1530256	0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs153546	0.81[CHD][hapmap]
rs153548	0.80[CHD][hapmap]
rs17285505	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1816769	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1866924	0.92[ASW][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];0.96[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1914	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.84[AFR][1000 genomes]
rs1968557	0.80[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1974786	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2019720	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2020383	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2099810	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2229992	0.95[CHB][hapmap];0.88[CHD][hapmap]
rs2251913	0.82[AFR][1000 genomes]
rs2289484	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs2431239	0.85[EUR][1000 genomes]
rs2431241	0.91[ASW][hapmap];0.85[CEU][hapmap];0.81[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes]
rs2431242	0.85[EUR][1000 genomes]
rs2431512	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs2431514	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2439589	0.85[EUR][1000 genomes]
rs2439595	0.95[CHB][hapmap]
rs2464803	0.92[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap]
rs2545156	0.84[ASW][hapmap];0.83[CHD][hapmap]
rs2545158	0.82[AFR][1000 genomes]
rs2546106	0.83[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2546107	0.82[AFR][1000 genomes]
rs2546108	0.91[ASW][hapmap];0.93[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs2546110	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2546112	0.90[CHB][hapmap]
rs2546117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2707763	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2707765	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes]
rs28578275	0.87[EUR][1000 genomes]
rs2900066	0.86[EUR][1000 genomes]
rs2901844	0.86[EUR][1000 genomes]
rs2909786	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2909787	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2909958	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs3317	0.92[ASW][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap]
rs35130225	0.86[EUR][1000 genomes]
rs35414976	0.85[EUR][1000 genomes]
rs374613	0.84[ASW][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap]
rs382427	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs3846716	0.89[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs390092	0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[AFR][1000 genomes]
rs395858	0.82[CHB][hapmap]
rs396321	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs4099181	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs414098	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs419155	0.92[ASW][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap]
rs448162	0.92[ASW][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap]
rs454886	0.90[CHB][hapmap]
rs458906	0.83[EUR][1000 genomes]
rs460137	0.84[ASW][hapmap];0.80[GIH][hapmap]
rs467033	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4705486	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4705559	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4705573	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4705608	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4705609	0.85[EUR][1000 genomes]
rs4705610	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4705815	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs4705816	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs511906	0.82[AFR][1000 genomes]
rs544243	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs548710	0.82[AFR][1000 genomes]
rs566419	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs569940	0.82[EUR][1000 genomes]
rs62364017	0.88[EUR][1000 genomes]
rs6594643	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs6594644	0.84[EUR][1000 genomes]
rs6594646	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6862050	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6864688	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs6867243	0.88[EUR][1000 genomes]
rs6879057	0.86[EUR][1000 genomes]
rs6893949	0.83[EUR][1000 genomes]
rs6894351	0.96[CEU][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs6898133	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs7704618	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7727738	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs861674	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs9326862	0.96[CEU][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs953916	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9647582	0.87[EUR][1000 genomes]
rs9647583	0.86[EUR][1000 genomes]
rs971517	0.84[EUR][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	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9326863	REEP5	cis	cerebellum	SCAN
rs9326863	NCRNA00219	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112044800-112058000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:112044800-112058800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:112045400-112062000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:112045600-112060200	Weak transcription	NHLF	lung
5	chr5:112045600-112061600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:112045600-112063600	Weak transcription	Ovary	ovary
7	chr5:112046000-112069200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:112047000-112060400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr5:112047000-112061600	Weak transcription	Aorta	Aorta
10	chr5:112047000-112066000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:112047400-112058600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr5:112047400-112060400	Weak transcription	Fetal Intestine Large	intestine
13	chr5:112047400-112072400	Weak transcription	Thymus	Thymus
14	chr5:112047600-112061600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:112048200-112058200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:112048400-112061200	Weak transcription	Fetal Intestine Small	intestine
17	chr5:112049200-112061600	Weak transcription	Fetal Stomach	stomach
18	chr5:112049600-112060400	Weak transcription	Lung	lung
19	chr5:112051200-112058600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:112052000-112072600	Weak transcription	Primary B cells from cord blood	blood
21	chr5:112052600-112072600	Weak transcription	Primary T cells from cord blood	blood
22	chr5:112054000-112056400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:112054400-112057400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:112054400-112058200	Weak transcription	Psoas Muscle	Psoas
25	chr5:112054400-112058400	Weak transcription	Left Ventricle	heart
26	chr5:112054400-112060600	Weak transcription	Small Intestine	intestine
27	chr5:112054400-112062200	Weak transcription	Right Ventricle	heart
28	chr5:112054400-112073200	Weak transcription	Pancreas	Pancrea
29	chr5:112054600-112057200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr5:112054600-112057200	Weak transcription	Brain Substantia Nigra	brain
31	chr5:112054600-112061400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr5:112054800-112057000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:112054800-112057400	Weak transcription	Colon Smooth Muscle	Colon
34	chr5:112054800-112058400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:112054800-112058600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr5:112054800-112060200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:112055000-112061600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr5:112055800-112056400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr5:112055800-112056400	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr5:112055800-112056400	Enhancers	Brain Anterior Caudate	brain
41	chr5:112055800-112056600	Enhancers	Brain Cingulate Gyrus	brain
42	chr5:112056000-112056400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr5:112056200-112056400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:112056200-112056400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr5:112056200-112056400	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr5:112056200-112056400	Enhancers	Brain Angular Gyrus	brain
47	chr5:112056200-112056400	Enhancers	Dnd41	blood
48	chr5:112056200-112056400	Flanking Active TSS	GM12878-XiMat	blood
49	chr5:112056200-112056600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr5:112056200-112056600	Enhancers	Duodenum Smooth Muscle	Duodenum

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