Variant report

Variant	rs12197948
Chromosome Location	chr6:45454844-45454845
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	chr6:45344833..45347447-chr6:45454271..45456836,2	K562	blood:
2	chr6:45450517..45452682-chr6:45454253..45456197,2	K562	blood:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10214519	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]
rs10485422	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10948237	1.00[JPT][hapmap]
rs10948238	1.00[JPT][hapmap]
rs11756145	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1200428	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12195878	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12204049	0.91[ASN][1000 genomes]
rs12209785	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12210100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215249	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1316330	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1317777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13201287	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13207392	1.00[JPT][hapmap]
rs13208741	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1343799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1928533	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1934327	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1934329	1.00[JPT][hapmap]
rs2031966	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2252718	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2256819	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2396442	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]
rs2677098	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2677099	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2677100	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2677109	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2677110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2790093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2790094	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2790095	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2790097	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2790098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2790099	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2790100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2790102	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs2790103	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2819852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2819853	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2819861	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2819864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2819865	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2819866	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2819867	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2820339	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2820340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4438954	1.00[JPT][hapmap]
rs4711816	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4714854	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]
rs4714859	0.86[ASN][1000 genomes]
rs6458443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6458445	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6458446	1.00[JPT][hapmap]
rs6458447	1.00[JPT][hapmap]
rs6904353	1.00[JPT][hapmap]
rs6905181	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6905847	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6911664	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6915569	1.00[JPT][hapmap]
rs6932037	0.82[ASN][1000 genomes]
rs72864634	0.91[ASN][1000 genomes]
rs765724	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7748231	1.00[JPT][hapmap]
rs7755257	1.00[JPT][hapmap]
rs7756144	0.95[EUR][1000 genomes]
rs7772562	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs910586	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9472494	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]
rs9885645	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12197948	RUNX2	cis	multi-tissue	Pritchard
rs12197948	RPL7L1	cis	cerebellum	SCAN
rs12197948	POLR1C	cis	cerebellum	SCAN
rs12197948	MRPL2	cis	cerebellum	SCAN
rs12197948	KLHDC3	cis	cerebellum	SCAN

Chromatin state (count:51 , 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	chr6:45445000-45466000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:45445800-45455400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:45445800-45457600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:45446400-45455200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:45447000-45456200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:45448400-45472000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:45448600-45455000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:45448800-45468400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:45449000-45455600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:45449000-45462800	Weak transcription	Primary B cells from cord blood	blood
13	chr6:45449000-45472600	Weak transcription	NHEK	skin
14	chr6:45449200-45461800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:45449600-45456600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:45450600-45459200	Weak transcription	NH-A	brain
17	chr6:45451400-45461800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:45451600-45455600	Weak transcription	Psoas Muscle	Psoas
19	chr6:45451800-45455200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:45451800-45455600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:45452000-45455600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:45452000-45472600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:45452400-45458400	Weak transcription	NHLF	lung
24	chr6:45452600-45456200	Weak transcription	Dnd41	blood
25	chr6:45452600-45459600	Weak transcription	HSMMtube	muscle
26	chr6:45452800-45455600	Weak transcription	Osteobl	bone
27	chr6:45452800-45459600	Weak transcription	NHDF-Ad	bronchial
28	chr6:45452800-45460000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:45453000-45458000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:45453800-45458200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr6:45454000-45456400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr6:45454000-45457600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:45454000-45457600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:45454000-45457800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:45454000-45458000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr6:45454000-45459800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:45454000-45471800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:45454200-45455000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr6:45454200-45456400	Enhancers	Primary B cells from peripheral blood	blood
40	chr6:45454200-45457600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr6:45454200-45459400	Enhancers	Primary T cells from cord blood	blood
42	chr6:45454400-45455200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:45454400-45455600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr6:45454400-45456400	Bivalent Enhancer	Fetal Thymus	thymus
45	chr6:45454400-45457200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:45454400-45457800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr6:45454600-45456000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr6:45454600-45459600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr6:45454800-45455400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:45454800-45455600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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