Variant report

Variant	rs302321
Chromosome Location	chr12:29928388-29928389
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29926045..29928762-chr12:29929311..29931905,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10843506	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843507	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs186216	0.85[AMR][1000 genomes]
rs302315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs302317	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs302340	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs302342	0.90[CEU][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs302344	1.00[LWK][hapmap];0.91[MKK][hapmap]
rs34924103	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs436124	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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs439639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs672107	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs721617	0.95[CEU][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7312697	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7970465	0.80[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.85[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs302321	TMTC1	cis	multi-tissue	Pritchard
rs302321	FGD4	cis	parietal	SCAN
rs302321	FGFR1OP2	cis	parietal	SCAN
rs302321	TMTC1	Cis_1M	lymphoblastoid	RTeQTL
rs302321	TMTC1	cis	Whole Blood	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29904200-29928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:29906600-29928400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:29916000-29931400	Weak transcription	Pancreas	Pancrea
4	chr12:29920400-29928400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr12:29921600-29934000	Weak transcription	Fetal Kidney	kidney
6	chr12:29922600-29929600	Weak transcription	HSMM	muscle
7	chr12:29922600-29931000	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:29922600-29931800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:29922600-29934000	Weak transcription	NHLF	lung
10	chr12:29922800-29930600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:29922800-29931200	Weak transcription	Aorta	Aorta
12	chr12:29922800-29933800	Weak transcription	Hela-S3	cervix
13	chr12:29924600-29931600	Weak transcription	Adipose Nuclei	Adipose
14	chr12:29925200-29928400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:29925400-29934000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:29925600-29934200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:29926000-29928400	Enhancers	Psoas Muscle	Psoas
18	chr12:29926200-29928400	Weak transcription	HMEC	breast
19	chr12:29926400-29929200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:29926400-29931400	Weak transcription	Ovary	ovary
21	chr12:29926400-29931600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:29926600-29931400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:29926800-29928600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:29926800-29929000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:29927000-29929600	Weak transcription	Left Ventricle	heart
26	chr12:29927000-29930800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:29927000-29931400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:29927200-29931400	Weak transcription	Fetal Heart	heart
29	chr12:29927200-29931800	Weak transcription	Right Atrium	heart
30	chr12:29927200-29931800	Weak transcription	Right Ventricle	heart
31	chr12:29927200-29931800	Weak transcription	Spleen	Spleen
32	chr12:29927400-29929400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
33	chr12:29927400-29930000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:29927600-29929400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
35	chr12:29927600-29929800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
36	chr12:29927600-29929800	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr12:29927800-29928600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:29927800-29929800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:29927800-29931000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:29928200-29929200	ZNF genes & repeats	Fetal Muscle Leg	muscle
41	chr12:29928200-29930000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:29928200-29930000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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