Variant report

Variant	rs10214519
Chromosome Location	chr6:45447558-45447559
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	chr6:45443101..45446352-chr6:45446405..45450040,4	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10485422	1.00[JPT][hapmap]
rs10948237	1.00[JPT][hapmap]
rs10948238	1.00[JPT][hapmap]
rs11756145	1.00[JPT][hapmap]
rs1200428	1.00[JPT][hapmap]
rs12195878	1.00[JPT][hapmap]
rs12197948	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12209785	1.00[JPT][hapmap]
rs12210100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12215249	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1316330	1.00[JPT][hapmap]
rs1317777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201287	1.00[JPT][hapmap]
rs13207392	1.00[JPT][hapmap]
rs1343799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1928533	1.00[JPT][hapmap]
rs1934327	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1934329	1.00[JPT][hapmap]
rs2031966	1.00[JPT][hapmap]
rs2252718	0.86[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2256819	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2396442	0.86[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2677098	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2677099	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2677100	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2677109	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2677110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790094	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2790095	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2790097	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2790098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790099	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790102	1.00[CEU][hapmap];0.88[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs2790103	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2819852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819865	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819866	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2819867	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2820339	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2820340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4438954	1.00[JPT][hapmap]
rs4711816	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4714854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs6458443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6458445	1.00[JPT][hapmap]
rs6458446	1.00[JPT][hapmap]
rs6458447	1.00[JPT][hapmap]
rs6904353	1.00[JPT][hapmap]
rs6905181	1.00[JPT][hapmap]
rs6905847	1.00[JPT][hapmap]
rs6911664	1.00[JPT][hapmap]
rs6915569	1.00[JPT][hapmap]
rs73737435	0.81[AFR][1000 genomes]
rs765724	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7748231	1.00[JPT][hapmap]
rs7755257	1.00[JPT][hapmap]
rs7756144	0.95[EUR][1000 genomes]
rs7772562	1.00[JPT][hapmap]
rs910586	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9472494	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]
rs9885645	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10214519	KLHDC3	cis	cerebellum	SCAN
rs10214519	MRPL2	cis	cerebellum	SCAN
rs10214519	RUNX2	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 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	chr6:45432200-45447800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:45436600-45447800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:45440400-45447800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:45440600-45448200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:45440800-45447800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:45441400-45447800	Weak transcription	Fetal Kidney	kidney
10	chr6:45441400-45448200	Weak transcription	Small Intestine	intestine
11	chr6:45442600-45448200	Weak transcription	Fetal Lung	lung
12	chr6:45444000-45448200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:45444200-45447600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:45444200-45448200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr6:45444800-45448800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr6:45444800-45449000	Enhancers	NHEK	skin
17	chr6:45445000-45448200	Weak transcription	Brain Hippocampus Middle	brain
18	chr6:45445000-45466000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:45445200-45448200	Weak transcription	Brain Anterior Caudate	brain
20	chr6:45445200-45448600	Genic enhancers	Primary hematopoietic stem cells	blood
21	chr6:45445400-45447800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:45445400-45448200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:45445600-45447600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:45445600-45447800	Enhancers	NHDF-Ad	bronchial
25	chr6:45445600-45448200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:45445800-45447600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:45445800-45448200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:45445800-45448200	Weak transcription	Esophagus	oesophagus
29	chr6:45445800-45448200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:45445800-45455400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr6:45445800-45457600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:45446000-45448200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:45446000-45449000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:45446200-45447600	Strong transcription	Dnd41	blood
35	chr6:45446200-45447800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:45446400-45447600	Weak transcription	Brain Substantia Nigra	brain
37	chr6:45446400-45447800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr6:45446400-45447800	Weak transcription	Brain Angular Gyrus	brain
39	chr6:45446400-45447800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr6:45446400-45447800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:45446400-45448200	Weak transcription	Primary T cells from cord blood	blood
42	chr6:45446400-45448200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr6:45446400-45454000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:45446400-45455200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr6:45446600-45447800	Weak transcription	Stomach Mucosa	stomach
46	chr6:45446600-45447800	Weak transcription	NH-A	brain
47	chr6:45446600-45448000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:45446600-45448000	Strong transcription	HSMM	muscle
49	chr6:45446600-45448000	Weak transcription	NHLF	lung
50	chr6:45446600-45448200	Weak transcription	Hela-S3	cervix

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