Variant report

Variant	rs1338298
Chromosome Location	chr1:210396062-210396063
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	chr1:210394665..210397584-chr1:210404970..210407618,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082497	Chromatin interaction
ENSG00000203706	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10863816	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119444	0.86[EUR][1000 genomes]
rs12239420	0.91[EUR][1000 genomes]
rs1473696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473813	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2473814	0.86[EUR][1000 genomes]
rs2487903	0.88[ASN][1000 genomes]
rs2494183	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]
rs2494184	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]
rs2494185	0.94[EUR][1000 genomes]
rs2494186	0.94[EUR][1000 genomes]
rs4844981	0.94[EUR][1000 genomes]
rs654523	1.00[YRI][hapmap]
rs677520	0.94[EUR][1000 genomes]
rs71571933	0.89[ASN][1000 genomes]
rs7534368	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs910109	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs910110	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9429839	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9430037	0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1338298	SLC30A1	cis	cerebellum	SCAN
rs1338298	SYT14	cis	parietal	SCAN
rs1338298	IRF6	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210395200-210397200	Enhancers	Rectal Smooth Muscle	rectum
2	chr1:210395400-210396200	Enhancers	Fetal Heart	heart
3	chr1:210395400-210396400	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr1:210395400-210396600	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr1:210395400-210396800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:210395400-210396800	Enhancers	NHEK	skin
7	chr1:210395600-210396400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:210395600-210396400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:210395600-210396800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr1:210395600-210396800	Enhancers	HSMMtube	muscle
11	chr1:210395600-210397000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:210395800-210396200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr1:210395800-210396800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:210395800-210396800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr1:210395800-210396800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:210395800-210396800	Enhancers	Colonic Mucosa	Colon
17	chr1:210395800-210396800	Enhancers	Fetal Muscle Leg	muscle
18	chr1:210395800-210397000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:210395800-210397200	Enhancers	Colon Smooth Muscle	Colon
20	chr1:210396000-210396200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:210396000-210396200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:210396000-210396600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:210396000-210396600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr1:210396000-210396800	Enhancers	NH-A	brain
25	chr1:210396000-210397000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:210396000-210397000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:210396000-210397200	Enhancers	Duodenum Mucosa	Duodenum
28	chr1:210396000-210397200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr1:210396000-210397200	Enhancers	Stomach Smooth Muscle	stomach
30	chr1:210396000-210397600	Enhancers	Fetal Kidney	kidney

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