Variant report

Variant	rs2513837
Chromosome Location	chr8:98936151-98936152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10091886	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs1020654	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs1020655	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs11779647	0.81[MEX][hapmap]
rs12548243	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs1378123	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs1378124	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs1378125	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[EUR][1000 genomes]
rs1378126	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs1454714	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap]
rs1840372	0.81[EUR][1000 genomes]
rs1968721	0.81[EUR][1000 genomes]
rs2256367	0.91[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2444900	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444903	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2444906	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2512071	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2512072	0.91[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513835	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2513836	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513838	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513839	0.87[CEU][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2959646	1.00[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap]
rs4298468	0.81[EUR][1000 genomes]
rs4469426	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4512352	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs5012370	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs6468603	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs897190	0.90[ASW][hapmap];0.93[CHD][hapmap];0.89[YRI][hapmap]
rs9693435	0.94[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1028055	chr8:98780445-98977746	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv891214	chr8:98849303-98990399	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv891215	chr8:98910287-98980663	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2513837	PGCP	cis	parietal	SCAN
rs2513837	NCALD	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:98929200-98944800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:98929600-98938000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr8:98929800-98936600	Weak transcription	Fetal Lung	lung
4	chr8:98929800-98937800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr8:98930800-98950000	Weak transcription	Right Ventricle	heart
6	chr8:98931000-98938600	Weak transcription	Placenta	Placenta
7	chr8:98931000-98940800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr8:98931200-98938000	Weak transcription	NH-A	brain
9	chr8:98931200-98938400	Weak transcription	Left Ventricle	heart
10	chr8:98931200-98944200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr8:98931600-98937800	Weak transcription	Fetal Intestine Large	intestine
12	chr8:98931600-98938200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr8:98931800-98943200	Enhancers	Fetal Muscle Leg	muscle
14	chr8:98932000-98940800	Weak transcription	Ovary	ovary
15	chr8:98932200-98943400	Weak transcription	Pancreas	Pancrea
16	chr8:98932400-98936400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr8:98932400-98940600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr8:98933000-98936800	Enhancers	Brain Hippocampus Middle	brain
19	chr8:98933200-98936400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr8:98934000-98937600	Weak transcription	Fetal Stomach	stomach
21	chr8:98934200-98943400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr8:98934600-98936800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr8:98934600-98938400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr8:98934800-98936200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr8:98934800-98936400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr8:98934800-98938800	Enhancers	Adipose Nuclei	Adipose
27	chr8:98935000-98936400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr8:98935000-98936400	Enhancers	NHDF-Ad	bronchial
29	chr8:98935200-98936800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr8:98935200-98937800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr8:98935200-98941200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr8:98935200-98941200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr8:98935200-98944400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr8:98935400-98937200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr8:98935400-98937800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr8:98935400-98937800	Weak transcription	Fetal Intestine Small	intestine
37	chr8:98935400-98937800	Weak transcription	Fetal Kidney	kidney
38	chr8:98935400-98938000	Weak transcription	Brain Substantia Nigra	brain
39	chr8:98935400-98938200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr8:98935400-98941200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr8:98935400-98941200	Weak transcription	Brain Anterior Caudate	brain
42	chr8:98935600-98937800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr8:98935800-98937800	Weak transcription	Osteobl	bone
44	chr8:98935800-98938200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr8:98935800-98938200	Weak transcription	Brain Angular Gyrus	brain
46	chr8:98935800-98941000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr8:98936000-98938200	Weak transcription	Right Atrium	heart

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