Variant report

Variant	rs436124
Chromosome Location	chr12:29916839-29916840
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	chr12:29914558..29917139-chr12:29921066..29923083,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10843506	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843507	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs186216	0.83[AMR][1000 genomes]
rs302315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302317	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302321	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]
rs302340	0.90[CEU][hapmap]
rs302342	0.90[CEU][hapmap];0.90[MEX][hapmap]
rs34924103	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs439639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672107	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs721617	0.95[CEU][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312697	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7970465	0.80[CHB][hapmap];0.87[JPT][hapmap];0.94[AFR][1000 genomes];0.89[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
rs436124	FGFR1OP2	cis	parietal	SCAN
rs436124	TMTC1	cis	multi-tissue	Pritchard
rs436124	TMTC1	Cis_1M	lymphoblastoid	RTeQTL
rs436124	TMTC1	cis	Whole Blood	GTEx
rs436124	FGD4	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29880000-29921200	Weak transcription	Fetal Kidney	kidney
2	chr12:29898600-29921200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:29904200-29928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:29904600-29927800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:29904800-29924200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:29906600-29928400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:29908800-29918800	Weak transcription	Hela-S3	cervix
8	chr12:29908800-29920800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:29908800-29925000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:29910400-29921400	Weak transcription	NHLF	lung
11	chr12:29910600-29921400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:29910600-29921400	Weak transcription	Osteobl	bone
13	chr12:29911000-29919200	Weak transcription	HMEC	breast
14	chr12:29911800-29922200	Weak transcription	Ovary	ovary
15	chr12:29912000-29921400	Weak transcription	Fetal Stomach	stomach
16	chr12:29912800-29924000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:29913200-29918800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:29913600-29917600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:29914800-29917000	Enhancers	Right Ventricle	heart
20	chr12:29914800-29917000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr12:29915200-29917000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr12:29915200-29917000	Enhancers	Colon Smooth Muscle	Colon
23	chr12:29915400-29917000	Enhancers	Adipose Nuclei	Adipose
24	chr12:29915600-29917000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr12:29915600-29917000	Enhancers	Psoas Muscle	Psoas
26	chr12:29915600-29918000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr12:29915600-29919800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:29915800-29917000	Strong transcription	Aorta	Aorta
29	chr12:29915800-29917000	Enhancers	Brain Hippocampus Middle	brain
30	chr12:29916000-29917000	Enhancers	H9 Cell Line	embryonic stem cell
31	chr12:29916000-29917000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr12:29916000-29917000	Genic enhancers	Spleen	Spleen
33	chr12:29916000-29917200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:29916000-29921800	Weak transcription	HSMMtube	muscle
35	chr12:29916000-29922400	Weak transcription	Esophagus	oesophagus
36	chr12:29916000-29931400	Weak transcription	Pancreas	Pancrea
37	chr12:29916200-29917000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:29916200-29917000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr12:29916200-29917000	Enhancers	Stomach Smooth Muscle	stomach
40	chr12:29916200-29922400	Weak transcription	Lung	lung
41	chr12:29916400-29917000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:29916400-29919000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:29916400-29919400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr12:29916400-29919600	Strong transcription	HSMM	muscle
45	chr12:29916400-29920200	Weak transcription	Brain Germinal Matrix	brain
46	chr12:29916400-29920800	Weak transcription	Brain Angular Gyrus	brain
47	chr12:29916400-29920800	Weak transcription	Fetal Lung	lung
48	chr12:29916400-29921800	Weak transcription	Brain Anterior Caudate	brain
49	chr12:29916600-29917200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:29916600-29919200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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