Variant report

Variant	rs17628742
Chromosome Location	chr13:39900598-39900599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10507479	1.00[ASN][1000 genomes]
rs12428000	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12583159	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583780	0.88[ASN][1000 genomes]
rs12585448	0.88[ASN][1000 genomes]
rs12585451	0.88[ASN][1000 genomes]
rs12585476	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17590635	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628476	0.88[ASN][1000 genomes]
rs17628483	0.88[ASN][1000 genomes]
rs17628519	0.88[ASN][1000 genomes]
rs17628771	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886171	1.00[ASN][1000 genomes]
rs2147130	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2324254	0.88[ASN][1000 genomes]
rs2324255	0.88[ASN][1000 genomes]
rs2324257	0.85[ASN][1000 genomes]
rs2875296	0.88[ASN][1000 genomes]
rs2875298	0.85[ASN][1000 genomes]
rs34485296	0.82[ASN][1000 genomes]
rs57158348	0.89[ASN][1000 genomes]
rs57251095	0.91[EUR][1000 genomes]
rs58017746	0.88[ASN][1000 genomes]
rs58501663	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59729125	1.00[ASN][1000 genomes]
rs60535758	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6563695	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7322148	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7336602	0.96[ASN][1000 genomes]
rs73451012	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73451015	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73467374	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74044033	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs768577	0.91[ASN][1000 genomes]
rs7990125	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7998423	0.89[EUR][1000 genomes]
rs8253	0.89[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036674	chr13:39841482-40008117	Bivalent Enhancer Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3420061	chr13:39896952-39901350	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39892200-39901200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr13:39897600-39902400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr13:39897800-39900600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:39899200-39901400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr13:39899200-39901600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr13:39899200-39901600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr13:39899400-39901000	Weak transcription	Fetal Kidney	kidney
8	chr13:39899400-39901200	Weak transcription	Right Atrium	heart
9	chr13:39899400-39901400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr13:39899400-39901400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:39899400-39901400	Weak transcription	Pancreas	Pancrea
12	chr13:39899400-39902400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr13:39899400-39902600	Weak transcription	Right Ventricle	heart
14	chr13:39899400-39904000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:39899400-39904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr13:39899400-39904000	Weak transcription	Gastric	stomach
17	chr13:39899400-39904800	Weak transcription	Left Ventricle	heart
18	chr13:39899600-39901600	Enhancers	Adipose Nuclei	Adipose
19	chr13:39899600-39903400	Weak transcription	Ovary	ovary
20	chr13:39900000-39901800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr13:39900400-39901200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr13:39900400-39901400	Enhancers	Fetal Lung	lung
23	chr13:39900400-39903600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr13:39900400-39906800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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