Variant report

Variant	rs9472494
Chromosome Location	chr6:45451836-45451837
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45344756..45346746-chr6:45450880..45452760,2	K562	blood:
2	chr6:45450517..45452682-chr6:45454253..45456197,2	K562	blood:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10214519	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10485422	1.00[JPT][hapmap]
rs10948236	0.81[ASN][1000 genomes]
rs10948237	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10948238	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11756145	1.00[JPT][hapmap]
rs1200428	1.00[JPT][hapmap]
rs12195878	1.00[JPT][hapmap]
rs12197948	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12209785	1.00[JPT][hapmap]
rs12210100	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12215249	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1316330	1.00[JPT][hapmap]
rs1317777	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13201287	1.00[JPT][hapmap]
rs13207392	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1343799	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1928533	1.00[JPT][hapmap]
rs1934327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1934329	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2031966	1.00[JPT][hapmap]
rs2252718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2256819	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2396442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2677098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677100	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677109	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2677110	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2790093	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2790094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2790095	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2790097	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2790098	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2790099	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2790100	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2790102	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2790103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2819852	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2819853	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2819861	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2819864	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2819865	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2819866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2819867	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2820339	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2820340	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4438954	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4711816	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs4714854	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458443	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6458445	1.00[JPT][hapmap]
rs6458446	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6458447	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6904353	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6905181	1.00[JPT][hapmap]
rs6905847	1.00[JPT][hapmap]
rs6911664	1.00[JPT][hapmap]
rs6915569	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs765724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7748231	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7755257	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7756094	0.84[ASN][1000 genomes]
rs7756144	0.99[EUR][1000 genomes]
rs7760160	0.84[ASN][1000 genomes]
rs7772562	1.00[JPT][hapmap]
rs910586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9885645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9472494	POLR1C	cis	cerebellum	SCAN
rs9472494	RPL7L1	cis	cerebellum	SCAN
rs9472494	KLHDC3	cis	cerebellum	SCAN
rs9472494	RUNX2	cis	multi-tissue	Pritchard
rs9472494	MRPL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45407200-45462000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:45419200-45456200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:45423000-45454400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:45445000-45466000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:45445800-45455400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr6:45445800-45457600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:45446400-45454000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:45446400-45455200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:45447000-45454000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:45447000-45456200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:45448400-45472000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:45448600-45455000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:45448800-45453600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:45448800-45453800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:45448800-45454200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr6:45448800-45454200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr6:45448800-45454200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:45448800-45454200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:45448800-45468400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:45449000-45452000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:45449000-45453800	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:45449000-45454400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:45449000-45454600	Weak transcription	HMEC	breast
24	chr6:45449000-45455600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:45449000-45462800	Weak transcription	Primary B cells from cord blood	blood
26	chr6:45449000-45472600	Weak transcription	NHEK	skin
27	chr6:45449200-45452200	Weak transcription	Dnd41	blood
28	chr6:45449200-45461800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:45449400-45452800	Enhancers	NHDF-Ad	bronchial
30	chr6:45449400-45453000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:45449400-45454200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:45449600-45454200	Weak transcription	Primary T cells from cord blood	blood
33	chr6:45449600-45454400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:45449600-45454400	Weak transcription	Brain Substantia Nigra	brain
35	chr6:45449600-45456600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:45450200-45452400	Enhancers	NHLF	lung
37	chr6:45450600-45452200	Enhancers	Fetal Lung	lung
38	chr6:45450600-45452600	Enhancers	HSMMtube	muscle
39	chr6:45450600-45459200	Weak transcription	NH-A	brain
40	chr6:45450800-45452000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:45450800-45452600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:45451000-45452000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:45451200-45452800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:45451200-45452800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:45451400-45452600	Flanking Active TSS	Osteobl	bone
46	chr6:45451400-45461800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:45451600-45453800	Weak transcription	HSMM	muscle
48	chr6:45451600-45455600	Weak transcription	Psoas Muscle	Psoas
49	chr6:45451800-45452000	Bivalent Enhancer	Fetal Thymus	thymus
50	chr6:45451800-45453000	Enhancers	Primary neutrophils fromperipheralblood	blood

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