Variant report

Variant	rs12740371
Chromosome Location	chr1:10254880-10254881
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	chr1:10254280..10257119-chr1:10269733..10271713,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054523	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10864448	0.80[ASN][1000 genomes]
rs11121526	0.87[ASN][1000 genomes]
rs12116966	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12728071	0.86[ASN][1000 genomes]
rs1974293	0.84[ASN][1000 genomes]
rs2027327	0.83[ASN][1000 genomes]
rs2027330	0.82[ASN][1000 genomes]
rs35257796	0.97[ASN][1000 genomes]
rs3828081	0.95[ASN][1000 genomes]
rs3903151	0.98[ASN][1000 genomes]
rs61775872	0.83[ASN][1000 genomes]
rs61784570	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6660928	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6670208	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6670320	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6675036	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12740371	KIF1B	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10233200-10258200	Weak transcription	Hela-S3	cervix
2	chr1:10236400-10258200	Weak transcription	HSMM	muscle
3	chr1:10240000-10255400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:10241000-10255600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:10241000-10257200	Weak transcription	Ovary	ovary
6	chr1:10241000-10258000	Weak transcription	Psoas Muscle	Psoas
7	chr1:10241200-10259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:10241400-10255600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:10244200-10256800	Weak transcription	Fetal Stomach	stomach
10	chr1:10247200-10255400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:10250000-10261000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:10250000-10269800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:10253800-10255400	Weak transcription	Placenta	Placenta
14	chr1:10254000-10257600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:10254400-10255200	Weak transcription	HepG2	liver
16	chr1:10254400-10255600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:10254400-10256800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:10254400-10257200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:10254600-10255800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:10254600-10255800	Enhancers	Osteobl	bone
21	chr1:10254600-10257000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:10254600-10257200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:10254800-10255200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:10254800-10258200	Weak transcription	NHDF-Ad	bronchial

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