Variant report

Variant	rs7623513
Chromosome Location	chr3:142100428-142100429
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11707154	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11708870	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11709758	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711164	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11711179	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11714244	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11714528	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11719737	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11720007	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11720762	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291363	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2306700	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55687115	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56088529	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56370391	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6769123	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6777420	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6780665	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73238130	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73238131	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73238136	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73238138	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73238140	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73238143	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73238144	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73238145	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73238148	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73238150	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73238152	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73238155	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73238158	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238159	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73238161	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73238169	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238173	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238176	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238185	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73238186	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73238187	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7633870	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7642634	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv520523	chr3:141818850-142110818	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	21 gene(s)	inside rSNPs	diseases
6	esv2763767	chr3:141820945-142101554	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7623513	XRN1	cis	brain	BrainEAC

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142046400-142112400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:142057400-142111400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:142059400-142111400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:142060800-142111200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr3:142063600-142104200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:142063600-142104600	Strong transcription	Placenta	Placenta
7	chr3:142063600-142111200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:142064600-142111400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr3:142066800-142115000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:142072400-142114600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:142074000-142113800	Weak transcription	HMEC	breast
12	chr3:142074600-142104000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:142075800-142101000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:142075800-142103600	Weak transcription	HSMMtube	muscle
15	chr3:142076000-142100800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:142076000-142103800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:142076000-142136400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:142076200-142101200	Weak transcription	Brain Substantia Nigra	brain
19	chr3:142076200-142104200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:142076800-142106000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:142076800-142106400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:142076800-142106600	Weak transcription	Spleen	Spleen
23	chr3:142076800-142120200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:142076800-142138200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:142077200-142106000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:142078800-142103600	Weak transcription	Fetal Heart	heart
27	chr3:142080000-142114000	Weak transcription	NHLF	lung
28	chr3:142083200-142106600	Weak transcription	Gastric	stomach
29	chr3:142083200-142113800	Weak transcription	Small Intestine	intestine
30	chr3:142083200-142114200	Weak transcription	A549	lung
31	chr3:142083400-142114800	Weak transcription	HepG2	liver
32	chr3:142083600-142101600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:142083600-142158600	Weak transcription	NHEK	skin
34	chr3:142084200-142103400	Weak transcription	NH-A	brain
35	chr3:142084600-142103200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:142086200-142111400	Strong transcription	Fetal Thymus	thymus
37	chr3:142088000-142100800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:142088200-142103800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:142088400-142103400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:142088400-142103400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:142089000-142104000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:142089600-142104400	Strong transcription	Fetal Intestine Large	intestine
43	chr3:142091000-142103800	Strong transcription	Adipose Nuclei	Adipose
44	chr3:142091600-142101600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:142091600-142108800	Weak transcription	Right Ventricle	heart
46	chr3:142091800-142106000	Weak transcription	Esophagus	oesophagus
47	chr3:142092000-142100800	Weak transcription	NHDF-Ad	bronchial
48	chr3:142092800-142104600	Strong transcription	Dnd41	blood
49	chr3:142092800-142111200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr3:142093000-142104200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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