Variant report

Variant	rs12897380
Chromosome Location	chr14:67964355-67964356
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	chr14:67960402..67962099-chr14:67962938..67964502,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10148645	0.96[ASN][1000 genomes]
rs1077989	0.91[ASN][1000 genomes]
rs10873201	0.97[ASN][1000 genomes]
rs10873202	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11158671	0.98[ASN][1000 genomes]
rs11158672	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878807	0.98[ASN][1000 genomes]
rs1885040	0.89[AFR][1000 genomes]
rs2004555	0.89[AFR][1000 genomes]
rs28373080	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72719193	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1035855	chr14:67935684-67964355	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1320	chr14:67938724-67984157	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12897380	MTHFD1	cis	cerebellum	SCAN
rs12897380	EIF2S1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67935000-67977200	Weak transcription	Brain Angular Gyrus	brain
2	chr14:67956000-67978000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr14:67956200-67981000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr14:67959400-67979800	Weak transcription	Fetal Brain Male	brain
5	chr14:67960600-67968400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr14:67961400-67972600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr14:67961400-67979400	Weak transcription	Primary B cells from cord blood	blood
8	chr14:67961400-67979400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr14:67961600-67964400	Weak transcription	Fetal Intestine Small	intestine
10	chr14:67961600-67964400	Weak transcription	Thymus	Thymus
11	chr14:67961600-67976800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:67961600-67979400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr14:67961800-67976400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr14:67962800-67979200	Weak transcription	Pancreas	Pancrea
15	chr14:67963800-67964800	Enhancers	Placenta	Placenta
16	chr14:67964000-67964600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr14:67964000-67965200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr14:67964000-67965200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr14:67964000-67965400	Enhancers	Primary T cells from cord blood	blood
20	chr14:67964000-67965400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr14:67964000-67970000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr14:67964200-67965000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr14:67964200-67965000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr14:67964200-67980800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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