Variant report

Variant	rs13065800
Chromosome Location	chr3:142251714-142251715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142251000..142253225-chr3:142255307..142257885,2	MCF-7	breast:
2	chr3:142248272..142250726-chr3:142251328..142253122,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10935463	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1129391	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11708470	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715514	0.85[EUR][1000 genomes]
rs11718899	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11916455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11923612	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11928203	0.85[ASW][hapmap]
rs12629001	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629713	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12634255	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12638158	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12639363	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13063075	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066441	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13068397	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13070239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13071750	0.85[CEU][hapmap]
rs13072346	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13072355	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13075259	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13082648	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs13085247	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13085261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13089219	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13092234	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13092593	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13093304	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13099184	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1485393	0.91[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs2140437	0.85[ASW][hapmap]
rs2227929	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2227931	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306699	0.91[CHB][hapmap]
rs34392719	0.85[CEU][hapmap];0.92[GIH][hapmap];0.89[TSI][hapmap]
rs3923464	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4256152	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4558780	0.86[EUR][1000 genomes]
rs4582075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683427	0.81[TSI][hapmap]
rs57299906	0.80[ASN][1000 genomes]
rs6440085	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6776402	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786320	0.89[CHB][hapmap]
rs6809448	0.85[ASW][hapmap];0.87[GIH][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap]
rs7432464	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7623785	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs7636909	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7641914	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7643377	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap]
rs7647329	0.91[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs953135	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs9814159	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs9829125	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs9859834	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs9867210	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap]

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	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
2	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
3	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
4	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
5	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
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv933680	chr3:142211643-142287189	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13065800	XRN1	cis	cerebellum	SCAN
rs13065800	TRPC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142200600-142271800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:142201600-142273200	Weak transcription	Esophagus	oesophagus
3	chr3:142201800-142273800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:142203000-142255200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:142203800-142255200	Weak transcription	Gastric	stomach
6	chr3:142204200-142253000	Weak transcription	Brain Substantia Nigra	brain
7	chr3:142204200-142273200	Weak transcription	Spleen	Spleen
8	chr3:142204200-142281400	Weak transcription	Colonic Mucosa	Colon
9	chr3:142209400-142271800	Weak transcription	HepG2	liver
10	chr3:142220200-142252400	Weak transcription	NHLF	lung
11	chr3:142220600-142253000	Weak transcription	HMEC	breast
12	chr3:142226000-142287200	Weak transcription	Right Ventricle	heart
13	chr3:142226400-142251800	Weak transcription	Lung	lung
14	chr3:142226600-142252200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:142228600-142252600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:142228600-142253000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:142231600-142255200	Weak transcription	Aorta	Aorta
18	chr3:142231600-142295800	Weak transcription	Small Intestine	intestine
19	chr3:142233000-142252000	Weak transcription	HUVEC	blood vessel
20	chr3:142233600-142255200	Weak transcription	Fetal Stomach	stomach
21	chr3:142233600-142271000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:142237800-142251800	Weak transcription	Hela-S3	cervix
23	chr3:142238600-142269000	Weak transcription	Fetal Intestine Small	intestine
24	chr3:142239800-142269600	Weak transcription	Thymus	Thymus
25	chr3:142240800-142252400	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:142240800-142281600	Weak transcription	Fetal Brain Male	brain
27	chr3:142241000-142251800	Weak transcription	Fetal Brain Female	brain
28	chr3:142241000-142251800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:142241000-142252800	Weak transcription	Left Ventricle	heart
30	chr3:142241000-142252800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:142241000-142254600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:142241000-142280800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:142241200-142253200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:142241600-142251800	Weak transcription	Fetal Lung	lung
35	chr3:142241600-142251800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:142241600-142252200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:142241800-142270800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:142242000-142251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:142242000-142252000	Weak transcription	HSMM	muscle
40	chr3:142242200-142251800	Weak transcription	Ovary	ovary
41	chr3:142242400-142275800	Weak transcription	NHEK	skin
42	chr3:142244400-142295600	Weak transcription	Fetal Heart	heart
43	chr3:142244800-142251800	Weak transcription	Pancreas	Pancrea
44	chr3:142244800-142252000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:142248200-142258400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:142248400-142269000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:142248400-142287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:142248600-142273600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:142249400-142253800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr3:142249400-142255600	Strong transcription	A549	lung

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