Variant report

Variant	rs13082648
Chromosome Location	chr3:142129008-142129009
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	chr3:142123276..142126061-chr3:142126798..142129776,3	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10935460	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10935462	0.85[ASN][1000 genomes]
rs11916455	0.91[CHB][hapmap]
rs12632726	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12695757	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13060437	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13061409	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13065140	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13067197	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13070239	0.90[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs13080394	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13085261	0.91[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs13087972	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13099184	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs1485393	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762799	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4256152	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap]
rs4582075	0.90[CHB][hapmap]
rs62276415	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786320	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7623785	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643377	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7647329	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs953135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814159	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836038	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9859834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9867210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2757892	chr3:141728870-142129836	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2759182	chr3:141728870-142129836	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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	nsv522549	chr3:141812759-142164735	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1000083	chr3:141956718-142172666	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv877557	chr3:142090402-142150204	Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13082648	PLS1	cis	parietal	SCAN
rs13082648	TRPC1	cis	parietal	SCAN
rs13082648	XRN1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142076000-142136400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:142076800-142138200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:142083600-142158600	Weak transcription	NHEK	skin
4	chr3:142105000-142151800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr3:142105800-142136600	Strong transcription	Fetal Intestine Large	intestine
6	chr3:142106800-142150800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:142109200-142141800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:142112200-142133200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr3:142112200-142145000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:142112200-142145400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:142112200-142151600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:142112200-142152000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:142112200-142152200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr3:142112200-142154600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr3:142112400-142142400	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr3:142112400-142146600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:142112600-142141600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:142112600-142150600	Strong transcription	Placenta	Placenta
19	chr3:142112800-142142800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:142113000-142152200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:142113400-142151800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:142113400-142151800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:142114800-142151800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:142115200-142129400	Weak transcription	Small Intestine	intestine
25	chr3:142115800-142134800	Weak transcription	Right Ventricle	heart
26	chr3:142115800-142136400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:142115800-142138000	Weak transcription	Esophagus	oesophagus
28	chr3:142116200-142129400	Weak transcription	NHLF	lung
29	chr3:142116400-142141800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:142117600-142138200	Weak transcription	Pancreas	Pancrea
31	chr3:142118800-142142400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:142119000-142143400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:142119800-142133000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:142119800-142142200	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:142120200-142145000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr3:142120400-142135400	Strong transcription	Liver	Liver
37	chr3:142120400-142142400	Strong transcription	Adipose Nuclei	Adipose
38	chr3:142120400-142151800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr3:142120600-142134400	Strong transcription	Primary hematopoietic stem cells	blood
40	chr3:142120600-142138000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:142120600-142151800	Strong transcription	Dnd41	blood
42	chr3:142120800-142134800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:142121200-142142600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:142121400-142140000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:142122400-142142800	Strong transcription	GM12878-XiMat	blood
46	chr3:142122800-142133400	Strong transcription	Primary B cells from cord blood	blood
47	chr3:142123200-142131000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr3:142123400-142130000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:142123400-142132400	Strong transcription	Fetal Muscle Leg	muscle
50	chr3:142123400-142134600	Strong transcription	Muscle Satellite Cultured Cells	--

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