Variant report

Variant	rs9847364
Chromosome Location	chr3:142155763-142155764
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142152079..142156407-chr3:142164108..142168187,4	MCF-7	breast:
2	chr3:142154895..142157522-chr3:142161051..142162570,2	K562	blood:
3	chr3:142153615..142157522-chr3:142160803..142162570,3	K562	blood:

Variant related genes	Relation type
ENSG00000114127	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10935461	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11711821	0.81[CEU][hapmap]
rs11925693	1.00[ASW][hapmap];0.96[CEU][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12695761	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13061823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13075471	0.89[EUR][1000 genomes]
rs1825522	0.82[EUR][1000 genomes]
rs2086933	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2171035	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2227928	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs2862743	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2862744	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2862745	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2862746	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28708455	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816805	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3922730	0.91[CHB][hapmap]
rs4273389	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4434160	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4441672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4597728	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4608715	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57177110	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440077	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6440078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440082	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440083	0.87[CHB][hapmap]
rs6440089	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs6440094	0.91[CHB][hapmap]
rs6769786	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6772400	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6775583	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6775718	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6777255	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6780250	0.91[CHB][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6782400	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs6782897	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6792259	0.91[CHB][hapmap]
rs6799752	0.91[CHB][hapmap]
rs6800695	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6802631	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7610557	0.91[CHB][hapmap]
rs7613664	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7625539	0.84[CEU][hapmap]
rs7627694	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7641330	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs7646701	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7651071	0.95[CHB][hapmap]
rs7652687	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]
rs9289647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9289648	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9816736	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9820770	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9821271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9826786	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9828178	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9846960	0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs9855140	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9861997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869842	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs9871402	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[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	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
3	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
4	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
5	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
6	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
7	nsv523596	chr3:142132749-142164735	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
9	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9847364	XRN1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142083600-142158600	Weak transcription	NHEK	skin
2	chr3:142127400-142159600	Weak transcription	Psoas Muscle	Psoas
3	chr3:142131600-142156000	Weak transcription	Fetal Heart	heart
4	chr3:142136400-142157400	Weak transcription	HMEC	breast
5	chr3:142138600-142158600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:142138600-142164600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:142138800-142163000	Weak transcription	Spleen	Spleen
8	chr3:142139400-142156200	Weak transcription	Small Intestine	intestine
9	chr3:142139400-142157000	Weak transcription	Brain Germinal Matrix	brain
10	chr3:142139400-142158600	Weak transcription	Pancreas	Pancrea
11	chr3:142139400-142163200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:142141200-142157000	Weak transcription	Esophagus	oesophagus
13	chr3:142141600-142162400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:142142200-142165400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:142146600-142164200	Weak transcription	Stomach Mucosa	stomach
16	chr3:142149000-142162600	Weak transcription	Brain Substantia Nigra	brain
17	chr3:142149800-142165000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:142150000-142156000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:142150000-142162000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:142150000-142162200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:142150000-142163200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:142150000-142164000	Weak transcription	NHDF-Ad	bronchial
23	chr3:142150000-142164400	Weak transcription	Aorta	Aorta
24	chr3:142150000-142164600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:142150200-142156200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:142150200-142156400	Weak transcription	Fetal Brain Female	brain
27	chr3:142150200-142156400	Weak transcription	NHLF	lung
28	chr3:142150200-142162000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:142150200-142162200	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:142150200-142162600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:142150200-142163200	Weak transcription	Colonic Mucosa	Colon
32	chr3:142150200-142164000	Weak transcription	Fetal Brain Male	brain
33	chr3:142150200-142164400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:142150200-142164400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:142150200-142164600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:142150200-142164600	Weak transcription	HSMMtube	muscle
37	chr3:142150400-142156200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr3:142150400-142158600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:142150400-142158600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:142150400-142158800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:142150400-142163000	Weak transcription	Lung	lung
42	chr3:142150400-142163800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:142150400-142164000	Weak transcription	Primary T cells from cord blood	blood
44	chr3:142150400-142164400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:142150400-142164400	Weak transcription	HSMM	muscle
46	chr3:142150400-142164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:142150400-142164600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:142150400-142164600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:142150600-142157000	Weak transcription	Placenta	Placenta
50	chr3:142150600-142162600	Weak transcription	Ovary	ovary

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