Variant report

Variant	rs10783318
Chromosome Location	chr12:39070576-39070577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10783392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10875966	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1095572	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1095574	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1386017	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1393536	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1393543	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1393544	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1601580	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1604559	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1604560	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1684412	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17119813	1.00[TSI][hapmap]
rs17124820	1.00[EUR][1000 genomes]
rs1968901	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2062759	1.00[CEU][hapmap]
rs2171221	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2630777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2630781	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2653728	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2653759	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2653768	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4768358	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7309754	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7971922	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs826843	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs826852	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs826877	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs826881	1.00[CEU][hapmap]
rs826883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs844116	1.00[CEU][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs905344	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs964721	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422488	chr12:38103874-39070734	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1039821	chr12:38959645-39121578	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1053316	chr12:38959645-39122853	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1043831	chr12:38979065-39117868	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv541479	chr12:38979065-39117868	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1045040	chr12:39038114-39084094	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10783318	CCL3	trans	brain	seeQTL
rs10783318	CCL3L1	trans	brain	seeQTL
rs10783318	CCL4	trans	brain	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39046000-39085400	Weak transcription	Aorta	Aorta
2	chr12:39046800-39080400	Weak transcription	Spleen	Spleen
3	chr12:39051600-39080400	Weak transcription	Lung	lung
4	chr12:39051600-39080800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:39054600-39071000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:39055800-39100800	Weak transcription	NHEK	skin
7	chr12:39056000-39080200	Weak transcription	Ovary	ovary
8	chr12:39056000-39092200	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
11	chr12:39056200-39078400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:39056200-39078400	Weak transcription	Adipose Nuclei	Adipose
13	chr12:39056200-39079000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:39056200-39080200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:39056800-39083000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:39057400-39083000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:39057600-39072200	Weak transcription	NHDF-Ad	bronchial
18	chr12:39058000-39077600	Weak transcription	HMEC	breast
19	chr12:39058200-39079000	Weak transcription	GM12878-XiMat	blood
20	chr12:39061200-39080400	Weak transcription	A549	lung
21	chr12:39061600-39080200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:39063200-39071800	Strong transcription	Liver	Liver
23	chr12:39063800-39080400	Weak transcription	Fetal Intestine Large	intestine
24	chr12:39063800-39082600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:39064800-39071200	Weak transcription	Esophagus	oesophagus
26	chr12:39065800-39072200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:39066200-39071400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr12:39066200-39114400	Weak transcription	Pancreas	Pancrea
29	chr12:39066600-39083400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:39066800-39071800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:39067000-39076600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:39068600-39076400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:39068800-39071000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:39069000-39071000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:39069000-39079000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:39069000-39080400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr12:39069400-39114600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:39069800-39076400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:39069800-39078600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:39069800-39083000	Weak transcription	Left Ventricle	heart

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