Variant report

Variant	rs12816393
Chromosome Location	chr12:29772059-29772060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29764406..29766975-chr12:29770947..29773354,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11829994	0.81[CEU][hapmap]
rs11837554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12310251	0.81[CEU][hapmap]
rs12312423	1.00[CHB][hapmap]
rs12422557	1.00[CHB][hapmap]
rs12423770	1.00[CHB][hapmap]
rs12423941	1.00[CHB][hapmap]
rs12424239	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12424502	1.00[CHB][hapmap]
rs12425004	1.00[CHB][hapmap]
rs12810686	1.00[CHB][hapmap]
rs12811228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813081	1.00[CHB][hapmap]
rs12822100	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12824107	1.00[CHB][hapmap]
rs12824420	1.00[CHB][hapmap]
rs12826187	1.00[CHB][hapmap]
rs12826210	1.00[CHB][hapmap]
rs12826633	1.00[CHB][hapmap]
rs12826893	0.86[CEU][hapmap]
rs12828728	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs159684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs159688	0.82[TSI][hapmap]
rs16934474	0.88[CEU][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs16934556	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs16934569	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs16934597	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs16934635	0.91[CEU][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1966531	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2288228	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs299484	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs34318689	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3825242	1.00[CHB][hapmap]
rs55807951	0.91[EUR][1000 genomes]
rs56178040	0.89[EUR][1000 genomes]
rs56367916	0.81[EUR][1000 genomes]
rs57072643	0.92[EUR][1000 genomes]
rs58290227	0.82[EUR][1000 genomes]
rs59519970	0.81[EUR][1000 genomes]
rs66750226	0.97[EUR][1000 genomes]
rs66849216	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67491988	0.85[EUR][1000 genomes]
rs73071556	0.81[EUR][1000 genomes]
rs73071582	0.82[EUR][1000 genomes]
rs73073417	0.96[EUR][1000 genomes]
rs73073419	0.96[EUR][1000 genomes]
rs7315541	1.00[JPT][hapmap]
rs7316470	1.00[CHB][hapmap]
rs74078415	0.81[EUR][1000 genomes]

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	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv870004	chr12:29762415-29825798	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12816393	SYT10	cis	cerebellum	SCAN
rs12816393	EMILIN1	trans	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29744400-29790800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:29744600-29791000	Weak transcription	Fetal Muscle Leg	muscle
3	chr12:29744800-29778200	Weak transcription	Ovary	ovary
4	chr12:29752600-29778200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:29760400-29787400	Weak transcription	Adipose Nuclei	Adipose
6	chr12:29761800-29778000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:29763000-29777400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:29763000-29777600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:29763200-29777600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:29763800-29773000	Weak transcription	Left Ventricle	heart
11	chr12:29763800-29778000	Weak transcription	Fetal Stomach	stomach
12	chr12:29763800-29786800	Weak transcription	Spleen	Spleen
13	chr12:29763800-29793600	Weak transcription	Right Ventricle	heart
14	chr12:29765000-29780800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:29765000-29786800	Weak transcription	HSMMtube	muscle
16	chr12:29765200-29773600	Weak transcription	Right Atrium	heart
17	chr12:29765200-29777600	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:29765200-29778200	Weak transcription	Aorta	Aorta
19	chr12:29765200-29785400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:29765400-29777400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:29765400-29777400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:29765400-29780800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:29765600-29802600	Weak transcription	Psoas Muscle	Psoas
24	chr12:29766400-29778600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:29766800-29773800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:29767600-29778000	Weak transcription	Fetal Kidney	kidney
27	chr12:29768800-29776400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:29769800-29772600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:29769800-29778400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:29770400-29792800	Weak transcription	NHLF	lung
31	chr12:29770600-29777800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:29770600-29780800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:29770600-29786600	Weak transcription	NHDF-Ad	bronchial
34	chr12:29770800-29781000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:29771000-29773000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:29771000-29773600	Weak transcription	HSMM	muscle
37	chr12:29771000-29778200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:29771000-29791800	Weak transcription	Hela-S3	cervix
39	chr12:29771200-29773200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:29771200-29786600	Weak transcription	HMEC	breast
41	chr12:29771600-29773200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:29771800-29772400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:29771800-29778200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:29771800-29778400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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