Variant report

Variant	rs4931217
Chromosome Location	chr12:29922821-29922822
allele	A/T
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: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10743672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743673	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743674	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771578	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10771579	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771580	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10843501	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10843502	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10843503	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843504	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11609828	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12231167	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12810794	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1551930	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2882467	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs302335	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs302336	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs302337	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs302338	0.92[AMR][1000 genomes]
rs4244848	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4244849	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931215	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4931218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931220	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56703053	0.81[AMR][1000 genomes]
rs67168837	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7967779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4931217	TMTC1	cis	Whole Blood	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29904200-29928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:29904600-29927800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:29904800-29924200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:29906600-29928400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:29908800-29925000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:29912800-29924000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:29916000-29931400	Weak transcription	Pancreas	Pancrea
8	chr12:29916600-29923000	Weak transcription	Liver	Liver
9	chr12:29916800-29924400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:29916800-29925400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:29917000-29924600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:29917000-29926000	Weak transcription	Right Ventricle	heart
13	chr12:29918000-29924800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:29919600-29924400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:29919800-29924400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:29919800-29924600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:29919800-29924600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:29919800-29926000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:29919800-29927600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr12:29920400-29928400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr12:29920800-29923600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr12:29921200-29926600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:29921400-29923400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:29921400-29924800	Enhancers	HMEC	breast
25	chr12:29921400-29927400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:29921600-29934000	Weak transcription	Fetal Kidney	kidney
27	chr12:29922000-29924600	Weak transcription	Brain Substantia Nigra	brain
28	chr12:29922600-29924600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:29922600-29924800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:29922600-29926000	Weak transcription	Ovary	ovary
31	chr12:29922600-29926400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:29922600-29926400	Weak transcription	Spleen	Spleen
33	chr12:29922600-29929600	Weak transcription	HSMM	muscle
34	chr12:29922600-29931000	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:29922600-29931800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:29922600-29934000	Weak transcription	NHLF	lung
37	chr12:29922800-29923200	Weak transcription	Fetal Heart	heart
38	chr12:29922800-29924000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:29922800-29924200	Weak transcription	Adipose Nuclei	Adipose
40	chr12:29922800-29924200	Weak transcription	NHDF-Ad	bronchial
41	chr12:29922800-29924400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:29922800-29924400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:29922800-29924400	Weak transcription	NHEK	skin
44	chr12:29922800-29924600	Weak transcription	Osteobl	bone
45	chr12:29922800-29926000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:29922800-29926000	Weak transcription	Left Ventricle	heart
47	chr12:29922800-29926000	Weak transcription	Psoas Muscle	Psoas
48	chr12:29922800-29926000	Weak transcription	Right Atrium	heart
49	chr12:29922800-29926000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:29922800-29928200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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