Variant report

Variant	rs7652687
Chromosome Location	chr3:142123276-142123277
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142115156..142117920-chr3:142121507..142123536,2	K562	blood:
2	chr3:142123276..142126061-chr3:142126798..142129776,3	K562	blood:
3	chr3:142121474..142124130-chr3:142126023..142128529,2	MCF-7	breast:
4	chr3:142116420..142117922-chr3:142120653..142123536,2	K562	blood:

Variant related genes	Relation type
ENSG00000251804	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10935461	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11711821	0.81[CEU][hapmap]
rs11925693	0.96[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12695761	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13061823	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13075471	0.89[EUR][1000 genomes]
rs1825522	0.83[EUR][1000 genomes]
rs2086933	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2171035	0.88[EUR][1000 genomes]
rs2227928	0.90[CHD][hapmap]
rs2862743	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2862744	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2862745	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2862746	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28708455	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816805	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4434160	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4441672	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4597728	0.80[EUR][1000 genomes]
rs4608715	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57177110	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440077	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6440078	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440082	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440089	0.91[CHD][hapmap]
rs6769786	0.87[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6772400	0.87[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6775583	0.80[EUR][1000 genomes]
rs6775718	0.80[EUR][1000 genomes]
rs6777255	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6780250	0.83[EUR][1000 genomes]
rs6782400	0.91[CHD][hapmap]
rs6782897	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6800695	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6802631	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613664	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7625539	0.84[CEU][hapmap]
rs7627694	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7641330	0.81[CEU][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs7646701	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7651071	0.82[CHB][hapmap]
rs9289647	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289648	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9816736	0.91[CHD][hapmap];0.83[EUR][1000 genomes]
rs9820770	0.83[EUR][1000 genomes]
rs9821271	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9826786	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9828178	0.83[EUR][1000 genomes]
rs9846960	0.88[CHD][hapmap];0.86[GIH][hapmap];0.81[TSI][hapmap]
rs9847364	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9855140	0.80[EUR][1000 genomes]
rs9861997	0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9869842	0.91[CHD][hapmap]
rs9871402	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7652687	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	chr3:142114600-142126600	Weak transcription	Fetal Heart	heart
24	chr3:142114800-142151800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:142115200-142126600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:142115200-142129400	Weak transcription	Small Intestine	intestine
27	chr3:142115800-142123400	Weak transcription	K562	blood
28	chr3:142115800-142125200	Weak transcription	Psoas Muscle	Psoas
29	chr3:142115800-142125400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:142115800-142125400	Weak transcription	Aorta	Aorta
31	chr3:142115800-142125400	Weak transcription	Lung	lung
32	chr3:142115800-142125400	Weak transcription	Spleen	Spleen
33	chr3:142115800-142126600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:142115800-142126600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:142115800-142126800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:142115800-142126800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:142115800-142127000	Weak transcription	Gastric	stomach
38	chr3:142115800-142128200	Weak transcription	Hela-S3	cervix
39	chr3:142115800-142134800	Weak transcription	Right Ventricle	heart
40	chr3:142115800-142136400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:142115800-142138000	Weak transcription	Esophagus	oesophagus
42	chr3:142116000-142123600	Weak transcription	Brain Germinal Matrix	brain
43	chr3:142116000-142126800	Weak transcription	A549	lung
44	chr3:142116000-142127000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:142116200-142123600	Weak transcription	Brain Angular Gyrus	brain
46	chr3:142116200-142125400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:142116200-142126400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:142116200-142129400	Weak transcription	NHLF	lung
49	chr3:142116400-142123400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:142116400-142125400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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