Variant report

Variant	rs16934870
Chromosome Location	chr12:29915778-29915779
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	chr12:29914558..29917139-chr12:29921066..29923083,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10843505	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11050423	0.85[GIH][hapmap];0.92[AMR][1000 genomes]
rs11050426	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050429	0.93[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11050430	1.00[ASW][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11050431	0.86[ASN][1000 genomes]
rs11050433	0.85[ASN][1000 genomes]
rs11050436	1.00[AFR][1000 genomes]
rs12370447	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2126891	1.00[ASW][hapmap]
rs36100969	0.85[ASN][1000 genomes]
rs60952280	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73077434	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73079425	1.00[AFR][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	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
2	nsv898953	chr12:29905322-29989292	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16934870	TMTC1	cis	multi-tissue	Pritchard
rs16934870	OVCH1	cis	parietal	SCAN
rs16934870	CCDC91	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29880000-29921200	Weak transcription	Fetal Kidney	kidney
2	chr12:29881600-29915800	Weak transcription	Brain Substantia Nigra	brain
3	chr12:29897200-29916000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:29898200-29915800	Weak transcription	Liver	Liver
5	chr12:29898600-29921200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:29901200-29915800	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:29902600-29915800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr12:29904200-29916000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:29904200-29928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:29904400-29915800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:29904400-29916800	Weak transcription	Gastric	stomach
12	chr12:29904600-29927800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:29904800-29924200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:29905000-29915800	Weak transcription	Lung	lung
15	chr12:29906600-29928400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:29908800-29918800	Weak transcription	Hela-S3	cervix
17	chr12:29908800-29920800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:29908800-29925000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:29909400-29916200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:29909800-29916000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:29910400-29921400	Weak transcription	NHLF	lung
22	chr12:29910600-29915800	Weak transcription	NHDF-Ad	bronchial
23	chr12:29910600-29921400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:29910600-29921400	Weak transcription	Osteobl	bone
25	chr12:29911000-29916000	Weak transcription	Spleen	Spleen
26	chr12:29911000-29919200	Weak transcription	HMEC	breast
27	chr12:29911600-29915800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:29911600-29915800	Weak transcription	Aorta	Aorta
29	chr12:29911800-29916200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:29911800-29916400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:29911800-29922200	Weak transcription	Ovary	ovary
32	chr12:29912000-29921400	Weak transcription	Fetal Stomach	stomach
33	chr12:29912800-29924000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:29913000-29915800	Strong transcription	HSMM	muscle
35	chr12:29913200-29918800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr12:29913600-29917600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:29914000-29916000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:29914800-29915800	Enhancers	Left Ventricle	heart
39	chr12:29914800-29917000	Enhancers	Right Ventricle	heart
40	chr12:29914800-29917000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr12:29915000-29916800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:29915000-29916800	Enhancers	Right Atrium	heart
43	chr12:29915000-29916800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr12:29915200-29916400	Enhancers	Fetal Brain Female	brain
45	chr12:29915200-29916600	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr12:29915200-29916800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr12:29915200-29917000	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr12:29915200-29917000	Enhancers	Colon Smooth Muscle	Colon
49	chr12:29915400-29916000	Enhancers	Fetal Brain Male	brain
50	chr12:29915400-29916600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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