Variant report

Variant	rs13403689
Chromosome Location	chr2:179084407-179084408
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179084247..179086331-chr2:179102848..179105496,2	K562	blood:
2	chr2:179082696..179084962-chr2:179087856..179090236,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10197166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930827	0.81[JPT][hapmap]
rs2366157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334002	0.82[CHB][hapmap]
rs334024	0.81[JPT][hapmap]
rs334028	0.80[JPT][hapmap]
rs334032	0.93[YRI][hapmap]
rs334035	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs334037	0.80[JPT][hapmap]
rs334042	0.84[CHD][hapmap]
rs334045	0.84[CHD][hapmap]
rs334102	0.86[JPT][hapmap]
rs334103	0.86[JPT][hapmap]
rs334110	0.86[JPT][hapmap]
rs6719178	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6731799	0.93[YRI][hapmap]
rs6747743	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73028670	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73028675	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7419749	0.81[JPT][hapmap]
rs7581504	1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1011423	chr2:179084407-179166160	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13403689	LOC100130691	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179076600-179087600	Weak transcription	Fetal Muscle Leg	muscle
2	chr2:179076600-179088000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:179077200-179088200	Weak transcription	Brain Anterior Caudate	brain
4	chr2:179077200-179089600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:179078600-179086200	Weak transcription	HMEC	breast
6	chr2:179078600-179091800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:179078800-179088400	Weak transcription	Brain Angular Gyrus	brain
8	chr2:179079000-179088200	Weak transcription	Fetal Brain Female	brain
9	chr2:179079000-179101200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:179081600-179085400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:179082800-179086000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:179083800-179085800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:179084000-179085600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
14	chr2:179084000-179086800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr2:179084200-179084600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:179084200-179084600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:179084200-179084600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
18	chr2:179084200-179084600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
19	chr2:179084200-179084800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr2:179084200-179085600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
21	chr2:179084400-179084600	Flanking Bivalent TSS/Enh	ES-WA7 Cell Line	embryonic stem cell
22	chr2:179084400-179084600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:179084400-179084600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
24	chr2:179084400-179084600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
25	chr2:179084400-179084600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
26	chr2:179084400-179084600	Enhancers	Brain Hippocampus Middle	brain
27	chr2:179084400-179084800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
28	chr2:179084400-179084800	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
29	chr2:179084400-179085200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:179084400-179088600	Weak transcription	Psoas Muscle	Psoas
31	chr2:179084400-179089200	Weak transcription	HSMM	muscle

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