Variant report

Variant	rs12209785
Chromosome Location	chr6:45506122-45506123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45498979..45501523-chr6:45505479..45508098,2	K562	blood:
2	chr6:45504338..45506736-chr6:45575272..45577741,2	MCF-7	breast:
3	chr6:45499803..45501981-chr6:45505161..45507219,2	MCF-7	breast:
4	chr6:45505637..45508807-chr6:45512620..45514671,3	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10214519	1.00[JPT][hapmap]
rs10485422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948237	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10948238	0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11756145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200428	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12195878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197948	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12204049	1.00[ASN][1000 genomes]
rs12210100	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12215249	0.85[ASN][1000 genomes]
rs1316330	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1317777	1.00[JPT][hapmap]
rs13201287	0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs13207392	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13208741	0.90[ASN][1000 genomes]
rs1928533	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1934327	1.00[JPT][hapmap]
rs1934329	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2031966	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396442	1.00[JPT][hapmap]
rs2677110	1.00[JPT][hapmap]
rs2790098	1.00[JPT][hapmap]
rs2819864	1.00[JPT][hapmap]
rs2819866	1.00[JPT][hapmap]
rs4438954	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4714854	1.00[JPT][hapmap]
rs4714859	0.95[ASN][1000 genomes]
rs6458445	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458446	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458447	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6904353	0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6905181	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905847	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911664	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915569	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6932037	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72864634	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748231	0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7754187	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs7755257	0.87[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7756094	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7760160	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7771889	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs7772562	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472494	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1019561	chr6:45485826-45535222	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv538214	chr6:45485826-45535222	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12209785	MRPL2	cis	cerebellum	SCAN
rs12209785	RPL7L1	cis	cerebellum	SCAN
rs12209785	ZNF318	cis	parietal	SCAN
rs12209785	RUNX2	cis	multi-tissue	Pritchard
rs12209785	KLHDC3	cis	cerebellum	SCAN
rs12209785	ENPP5	cis	lymphoblastoid	seeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45465000-45521600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr6:45481400-45514600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:45482800-45514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:45484400-45509400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr6:45484400-45514600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:45489000-45521800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:45493200-45516200	Weak transcription	Hela-S3	cervix
8	chr6:45497400-45506400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:45498000-45507800	Weak transcription	Fetal Thymus	thymus
10	chr6:45498600-45514600	Weak transcription	Dnd41	blood
11	chr6:45500200-45513800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:45500600-45506400	Weak transcription	Gastric	stomach
13	chr6:45500600-45508000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:45500600-45514600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:45500600-45516600	Weak transcription	Small Intestine	intestine
16	chr6:45501200-45507800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:45501200-45510600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:45501400-45506200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:45501400-45506400	Weak transcription	Liver	Liver
20	chr6:45501400-45507800	Weak transcription	Psoas Muscle	Psoas
21	chr6:45501400-45508000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:45501400-45509600	Strong transcription	HSMM	muscle
23	chr6:45501600-45509400	Weak transcription	HSMMtube	muscle
24	chr6:45501600-45509800	Weak transcription	NHLF	lung
25	chr6:45502000-45516200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:45503000-45514600	Weak transcription	Esophagus	oesophagus
27	chr6:45504200-45506800	Weak transcription	Fetal Intestine Small	intestine
28	chr6:45504200-45509400	Weak transcription	K562	blood
29	chr6:45504200-45514600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:45504400-45506800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:45504400-45509400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:45504600-45508000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:45504600-45513200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:45504800-45507200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:45504800-45507200	Enhancers	NHDF-Ad	bronchial
36	chr6:45505000-45506400	Weak transcription	Stomach Mucosa	stomach
37	chr6:45505000-45509800	Weak transcription	NH-A	brain
38	chr6:45505000-45510800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:45505400-45506200	Weak transcription	Osteobl	bone
40	chr6:45505400-45506800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:45505400-45507400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:45505400-45509000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr6:45505400-45512200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:45505600-45508200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:45505800-45506200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:45505800-45506600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:45505800-45507000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr6:45506000-45506200	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr6:45506000-45506400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:45506000-45506600	Enhancers	Fetal Lung	lung

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