Variant report

Variant	rs2396442
Chromosome Location	chr6:45456981-45456982
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	chr6:44709340..44711190-chr6:45455747..45458398,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10214519	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]
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];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.97[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];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12215249	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.99[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];0.92[EUR][1000 genomes]
rs13201287	1.00[JPT][hapmap]
rs13207392	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13208741	0.84[AMR][1000 genomes]
rs1343799	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1928533	1.00[JPT][hapmap]
rs1934327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2256819	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2677098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677100	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677109	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2677110	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2790093	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2790094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2790095	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2790097	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2790098	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2790099	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2790100	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2790102	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2790103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2819852	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2819853	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2819861	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2819864	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2819865	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2819866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2819867	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2820339	1.00[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2820340	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4438954	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4711816	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4714854	0.86[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6458443	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[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];0.88[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	0.93[EUR][1000 genomes]
rs7760160	0.84[ASN][1000 genomes]
rs7772562	1.00[JPT][hapmap]
rs910586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9472494	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]
rs9885645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[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
rs2396442	MRPL2	cis	cerebellum	SCAN
rs2396442	RPL7L1	cis	cerebellum	SCAN
rs2396442	KLHDC3	cis	cerebellum	SCAN
rs2396442	RUNX2	cis	multi-tissue	Pritchard
rs2396442	POLR1C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45407200-45462000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:45445000-45466000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:45445800-45457600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:45448400-45472000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:45448800-45468400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:45449000-45462800	Weak transcription	Primary B cells from cord blood	blood
7	chr6:45449000-45472600	Weak transcription	NHEK	skin
8	chr6:45449200-45461800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:45450600-45459200	Weak transcription	NH-A	brain
10	chr6:45451400-45461800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:45452000-45472600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:45452400-45458400	Weak transcription	NHLF	lung
13	chr6:45452600-45459600	Weak transcription	HSMMtube	muscle
14	chr6:45452800-45459600	Weak transcription	NHDF-Ad	bronchial
15	chr6:45452800-45460000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:45453000-45458000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:45453800-45458200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr6:45454000-45457600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:45454000-45457600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:45454000-45457800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:45454000-45458000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr6:45454000-45459800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:45454000-45471800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:45454200-45457600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr6:45454200-45459400	Enhancers	Primary T cells from cord blood	blood
26	chr6:45454400-45457200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:45454400-45457800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr6:45454600-45459600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr6:45455000-45459600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr6:45455200-45457200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:45455200-45459000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:45455400-45458000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:45455600-45457400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr6:45455600-45458000	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr6:45455600-45467200	Strong transcription	HSMM	muscle
36	chr6:45455800-45457800	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr6:45455800-45459800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:45456000-45457800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:45456200-45457000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:45456200-45457600	Enhancers	Dnd41	blood
41	chr6:45456200-45458200	Enhancers	Primary T cells fromperipheralblood	blood
42	chr6:45456400-45457200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:45456400-45457400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:45456400-45457600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:45456400-45457800	Bivalent Enhancer	Thymus	Thymus
46	chr6:45456400-45458000	Enhancers	Fetal Thymus	thymus
47	chr6:45456600-45457000	Weak transcription	Osteobl	bone
48	chr6:45456600-45457400	Genic enhancers	Primary hematopoietic stem cells	blood
49	chr6:45456600-45457600	Enhancers	K562	blood
50	chr6:45456600-45458800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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