Variant report

Variant	rs17803662
Chromosome Location	chr13:39969261-39969262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1010912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1010913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10467465	0.88[GIH][hapmap]
rs12585795	1.00[JPT][hapmap]
rs1535776	1.00[YRI][hapmap]
rs17059768	1.00[CHB][hapmap]
rs17059793	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17229177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17229842	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1752055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182779	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs516214	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs59118983	0.94[ASN][1000 genomes]
rs59279878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60354480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs629011	1.00[YRI][hapmap]
rs629373	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73453087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73453091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73456912	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73456919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73456925	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73456930	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73456942	0.94[ASN][1000 genomes]
rs9315682	1.00[ASW][hapmap]
rs9315683	1.00[ASW][hapmap]
rs9532377	1.00[CHB][hapmap]
rs9594331	1.00[CHD][hapmap];0.88[GIH][hapmap]
rs9603530	1.00[CHD][hapmap];0.88[GIH][hapmap]
rs9603532	1.00[ASW][hapmap]

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	nsv900008	chr13:39962791-40020267	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17803662	PRAC	trans	lymphoblastoid	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39960000-39979200	Weak transcription	NHDF-Ad	bronchial
2	chr13:39966600-39970000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr13:39967600-39969400	Enhancers	Brain Substantia Nigra	brain
4	chr13:39967600-39970400	Enhancers	Left Ventricle	heart
5	chr13:39968200-39973200	Enhancers	Right Ventricle	heart
6	chr13:39968400-39969800	Weak transcription	Spleen	Spleen
7	chr13:39968400-39970200	Enhancers	Fetal Heart	heart
8	chr13:39968400-39970400	Enhancers	Placenta Amnion	Placenta Amnion
9	chr13:39968600-39970200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr13:39968600-39970400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr13:39968800-39970000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr13:39968800-39970000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:39968800-39970000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr13:39968800-39970000	Active TSS	Aorta	Aorta
15	chr13:39968800-39970200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr13:39968800-39970200	Enhancers	Brain Cingulate Gyrus	brain
17	chr13:39968800-39970400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:39968800-39970400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr13:39968800-39970400	Enhancers	Adipose Nuclei	Adipose
20	chr13:39968800-39970400	Enhancers	Brain Anterior Caudate	brain
21	chr13:39968800-39970400	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr13:39968800-39972400	Enhancers	Fetal Lung	lung
23	chr13:39969000-39969400	Flanking Active TSS	Right Atrium	heart
24	chr13:39969000-39969600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr13:39969000-39969600	Enhancers	Brain Germinal Matrix	brain
26	chr13:39969000-39970000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr13:39969000-39970000	Enhancers	Brain Hippocampus Middle	brain
28	chr13:39969000-39970000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr13:39969000-39970000	Enhancers	Osteobl	bone
30	chr13:39969000-39970200	Enhancers	Fetal Brain Male	brain
31	chr13:39969000-39970400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr13:39969000-39970400	Enhancers	Fetal Muscle Trunk	muscle
33	chr13:39969000-39970400	Enhancers	Placenta	Placenta
34	chr13:39969200-39969400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr13:39969200-39969600	Active TSS	Ovary	ovary
36	chr13:39969200-39970000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
37	chr13:39969200-39970000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:39969200-39970000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr13:39969200-39970000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr13:39969200-39970600	Enhancers	Fetal Kidney	kidney
41	chr13:39969200-39972800	Enhancers	Fetal Muscle Leg	muscle

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