Variant report

Variant	rs9326862
Chromosome Location	chr5:112054547-112054548
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112053751..112055842-chr5:112072998..112075540,2	K562	blood:
2	chr5:112053504..112055952-chr5:112056185..112057959,2	MCF-7	breast:
3	chr5:112053239..112054814-chr5:112058793..112060310,2	K562	blood:
4	chr5:112050398..112055694-chr5:112065977..112068837,5	K562	blood:
5	chr5:112053751..112057397-chr5:112071808..112074498,3	K562	blood:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10051624	0.84[EUR][1000 genomes]
rs10071425	0.82[EUR][1000 genomes]
rs10073398	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10075281	0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs10075323	0.83[EUR][1000 genomes]
rs10075377	0.83[EUR][1000 genomes]
rs10076641	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10213844	0.84[EUR][1000 genomes]
rs10463643	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs1093677	0.90[CHD][hapmap]
rs11241182	0.89[CEU][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11241183	0.84[EUR][1000 genomes]
rs11241184	0.90[EUR][1000 genomes]
rs11241185	0.81[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs11749632	0.84[EUR][1000 genomes]
rs11749701	0.88[EUR][1000 genomes]
rs11954856	0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12513787	0.83[EUR][1000 genomes]
rs12513804	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12518091	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12658609	0.85[EUR][1000 genomes]
rs12659119	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12719151	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13156251	0.80[EUR][1000 genomes]
rs1441375	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1465910	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs151977	0.88[CHD][hapmap]
rs1661035	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1661036	0.88[ASN][1000 genomes]
rs1816769	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1914	0.82[CEU][hapmap]
rs1974786	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2019720	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs2020383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2289484	0.89[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs2431239	0.83[EUR][1000 genomes]
rs2431241	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs2431242	0.89[EUR][1000 genomes]
rs2431512	0.85[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2439589	0.83[EUR][1000 genomes]
rs2439591	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2464803	0.85[TSI][hapmap]
rs2545162	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs2545165	0.86[CHB][hapmap]
rs2545167	0.88[CHD][hapmap]
rs2546106	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs2546108	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs2546117	0.83[EUR][1000 genomes]
rs2707763	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs2707765	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs28578275	0.84[EUR][1000 genomes]
rs2900066	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2901844	0.83[EUR][1000 genomes]
rs2909786	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[EUR][1000 genomes]
rs2909787	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[EUR][1000 genomes]
rs2909958	0.96[CEU][hapmap];0.93[CHB][hapmap];0.86[EUR][1000 genomes]
rs2952615	0.86[CHB][hapmap]
rs35130225	0.89[EUR][1000 genomes]
rs351771	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs35414976	0.83[EUR][1000 genomes]
rs382260	0.88[CHD][hapmap]
rs3846716	0.92[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs396321	0.92[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4099181	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41115	0.93[CHB][hapmap];0.88[CHD][hapmap]
rs411356	0.93[CHB][hapmap];0.87[CHD][hapmap]
rs414098	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs42427	0.93[CHB][hapmap];0.88[CHD][hapmap]
rs429427	0.88[CHD][hapmap]
rs430665	0.88[CHD][hapmap]
rs458906	0.81[EUR][1000 genomes]
rs464002	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs464708	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs465454	0.88[CHD][hapmap]
rs465899	0.93[CHB][hapmap];0.88[CHD][hapmap]
rs467033	0.85[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs468179	0.88[ASN][1000 genomes]
rs4705486	0.81[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs4705559	0.85[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs4705573	0.83[EUR][1000 genomes]
rs4705608	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs4705609	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4705610	0.85[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs4705624	0.84[EUR][1000 genomes]
rs4705815	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4705816	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs497844	0.88[CHD][hapmap]
rs544243	0.89[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs569940	0.85[EUR][1000 genomes]
rs62364017	0.86[EUR][1000 genomes]
rs6594643	0.85[CEU][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6594644	0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6594646	0.85[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs6862050	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs6864688	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867243	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6879057	0.83[EUR][1000 genomes]
rs6894351	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6898133	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs712662	0.88[CHD][hapmap]
rs712665	0.88[CHD][hapmap]
rs7704618	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs861674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs866006	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs9326863	0.96[CEU][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs953916	0.85[EUR][1000 genomes]
rs9647582	0.84[EUR][1000 genomes]
rs9647583	0.83[EUR][1000 genomes]
rs971517	0.83[AMR][1000 genomes];0.88[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9326862	NCRNA00219	cis	parietal	SCAN
rs9326862	REEP5	cis	cerebellum	SCAN
rs9326862	CDO1	cis	cerebellum	SCAN

Chromatin state (count:63 , 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	chr5:112045600-112054600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:112045600-112060200	Weak transcription	NHLF	lung
6	chr5:112045600-112061600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:112045600-112063600	Weak transcription	Ovary	ovary
8	chr5:112046000-112069200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:112047000-112060400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr5:112047000-112061600	Weak transcription	Aorta	Aorta
11	chr5:112047000-112066000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:112047400-112056200	Weak transcription	Dnd41	blood
13	chr5:112047400-112058600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:112047400-112060400	Weak transcription	Fetal Intestine Large	intestine
15	chr5:112047400-112072400	Weak transcription	Thymus	Thymus
16	chr5:112047600-112061600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr5:112048200-112058200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:112048400-112061200	Weak transcription	Fetal Intestine Small	intestine
19	chr5:112049200-112061600	Weak transcription	Fetal Stomach	stomach
20	chr5:112049600-112055800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr5:112049600-112060400	Weak transcription	Lung	lung
22	chr5:112050200-112056200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr5:112050800-112056200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr5:112051000-112056200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr5:112051200-112058600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:112052000-112072600	Weak transcription	Primary B cells from cord blood	blood
27	chr5:112052600-112072600	Weak transcription	Primary T cells from cord blood	blood
28	chr5:112052800-112055800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr5:112053000-112054600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr5:112053200-112054600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr5:112053200-112054600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:112053200-112054800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr5:112053400-112054600	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr5:112053400-112054600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr5:112053400-112054600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:112053400-112055000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr5:112053800-112055000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr5:112054000-112054600	Enhancers	H1 Cell Line	embryonic stem cell
39	chr5:112054000-112054600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:112054000-112054600	Enhancers	Brain Angular Gyrus	brain
41	chr5:112054000-112054600	Enhancers	Brain Substantia Nigra	brain
42	chr5:112054000-112054600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr5:112054000-112054800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:112054000-112054800	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr5:112054000-112054800	Enhancers	Brain Cingulate Gyrus	brain
46	chr5:112054000-112054800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:112054000-112055000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr5:112054000-112056400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:112054200-112054600	Enhancers	Brain Hippocampus Middle	brain
50	chr5:112054200-112054800	Enhancers	Brain Anterior Caudate	brain

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