Variant report

Variant	rs12889206
Chromosome Location	chr14:68769182-68769183
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	chr14:68764415..68769564-chr14:68770855..68774967,6	MCF-7	breast:
2	chr14:68765970..68770223-chr14:69260401..69262573,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1570106	0.86[CEU][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1810623	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2208397	0.90[GIH][hapmap]
rs2331703	1.00[MEX][hapmap]
rs2331704	1.00[MEX][hapmap]
rs2525507	1.00[MEX][hapmap]
rs2588827	0.85[MEX][hapmap]
rs2753403	0.86[MEX][hapmap]
rs2842320	0.86[MEX][hapmap]
rs3784106	0.82[LWK][hapmap]
rs4899243	0.85[MEX][hapmap]
rs4902564	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4902567	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902571	1.00[MEX][hapmap]
rs6573834	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7150454	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7160221	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72727425	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8003738	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8008961	0.90[GIH][hapmap]
rs8009876	1.00[MEX][hapmap]
rs8015516	0.86[MEX][hapmap]

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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv428628	chr14:68674504-68835127	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12889206	MTHFD1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68760400-68776800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:68760600-68773600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr14:68762000-68773400	Weak transcription	Small Intestine	intestine
4	chr14:68762800-68771400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr14:68763400-68772400	Weak transcription	Pancreas	Pancrea
6	chr14:68765000-68774600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr14:68765200-68771000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr14:68767600-68776400	Weak transcription	Left Ventricle	heart
9	chr14:68768000-68771000	Weak transcription	Fetal Heart	heart
10	chr14:68768200-68772600	Weak transcription	Ovary	ovary
11	chr14:68768400-68769200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr14:68768400-68769400	ZNF genes & repeats	Fetal Thymus	thymus
13	chr14:68768600-68769200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
14	chr14:68768800-68769200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:68768800-68769200	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr14:68768800-68769200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
17	chr14:68768800-68769200	ZNF genes & repeats	Fetal Lung	lung
18	chr14:68768800-68769200	ZNF genes & repeats	Dnd41	blood
19	chr14:68768800-68770000	ZNF genes & repeats	Fetal Muscle Leg	muscle
20	chr14:68769000-68769600	Weak transcription	A549	lung
21	chr14:68769000-68773400	Weak transcription	Aorta	Aorta
22	chr14:68769000-68776400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr14:68769000-68810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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