Variant report

Variant	rs3818242
Chromosome Location	chr14:67970188-67970189
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	chr14:67968272..67970276-chr14:67989655..67991450,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10133655	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10144299	0.92[ASN][1000 genomes]
rs10873203	0.92[ASN][1000 genomes]
rs11622515	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11622608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626771	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11626910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11850406	0.87[ASN][1000 genomes]
rs12881607	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17093620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61988189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988190	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6573776	0.89[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][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	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
6	nsv826970	chr14:67966521-67971459	Enhancers Weak transcription Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3818242	GALNTL1	cis	cerebellum	SCAN
rs3818242	ACTN1	cis	parietal	SCAN
rs3818242	KCNH5	cis	cerebellum	SCAN
rs3818242	EIF2S1	cis	cerebellum	SCAN
rs3818242	MTHFD1	cis	cerebellum	SCAN
rs3818242	LINGO4	trans	parietal	SCAN

Chromatin state (count:31 , 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	chr14:67961400-67972600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr14:67961400-67979400	Weak transcription	Primary B cells from cord blood	blood
7	chr14:67961400-67979400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr14:67961600-67976800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr14:67961600-67979400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr14:67961800-67976400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr14:67962800-67979200	Weak transcription	Pancreas	Pancrea
12	chr14:67964200-67980800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr14:67965000-67979400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr14:67965000-67980200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr14:67965200-67980200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr14:67965400-67980800	Weak transcription	Primary T cells from cord blood	blood
17	chr14:67968200-67973000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr14:67968200-67973000	Weak transcription	NHEK	skin
19	chr14:67968800-67980400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr14:67969400-67970400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr14:67969600-67970200	Enhancers	Fetal Intestine Small	intestine
22	chr14:67969600-67970200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr14:67969800-67970200	Enhancers	Liver	Liver
24	chr14:67969800-67970200	Enhancers	Duodenum Mucosa	Duodenum
25	chr14:67969800-67970200	Enhancers	Hela-S3	cervix
26	chr14:67970000-67970200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr14:67970000-67970200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr14:67970000-67970200	Enhancers	Fetal Intestine Large	intestine
29	chr14:67970000-67970200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr14:67970000-67970400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr14:67970000-67970400	Enhancers	Placenta	Placenta

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