Variant report

Variant	rs7647573
Chromosome Location	chr3:142251583-142251584
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	chr3:142251000..142253225-chr3:142255307..142257885,2	MCF-7	breast:
2	chr3:142248272..142250726-chr3:142251328..142253122,2	K562	blood:

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10935461	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs10935465	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1129393	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11925693	0.93[CHD][hapmap];0.82[GIH][hapmap]
rs13061823	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs13065075	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13067795	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069307	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13075471	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13079246	0.81[CEU][hapmap]
rs13085998	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093869	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13098343	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1357529	0.82[EUR][1000 genomes]
rs1357530	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs16852486	0.81[CEU][hapmap]
rs1916639	0.84[EUR][1000 genomes]
rs1983434	0.92[CEU][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs1983435	0.84[EUR][1000 genomes]
rs2030613	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2049325	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs2049326	0.85[EUR][1000 genomes]
rs2140432	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs2177396	0.85[EUR][1000 genomes]
rs2227928	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2227930	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2354860	0.83[EUR][1000 genomes]
rs28617475	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2862743	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs2862745	0.91[CHB][hapmap];0.93[CHD][hapmap]
rs2883380	0.81[CEU][hapmap]
rs3816805	0.86[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap]
rs3922730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4273389	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4413348	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs4441672	0.91[CHB][hapmap]
rs4597728	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4683690	0.81[CEU][hapmap]
rs6414350	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440078	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[YRI][hapmap]
rs6440082	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[YRI][hapmap]
rs6440086	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440087	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440088	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440089	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440090	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440091	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440092	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440093	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440098	0.92[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs6440099	0.84[EUR][1000 genomes]
rs6768093	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6769786	0.91[CHB][hapmap]
rs6770155	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6772400	0.91[CHB][hapmap]
rs6775583	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6775718	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6775813	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs6780250	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6782400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6783203	0.84[EUR][1000 genomes]
rs6784089	0.84[EUR][1000 genomes]
rs6785675	0.89[EUR][1000 genomes]
rs6789958	0.80[CEU][hapmap]
rs6791816	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6793735	0.81[CEU][hapmap]
rs6798232	0.81[CEU][hapmap]
rs6799752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6802631	0.86[CHB][hapmap]
rs6802774	0.80[EUR][1000 genomes]
rs6808205	0.81[CEU][hapmap]
rs7428496	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7430429	0.81[CEU][hapmap]
rs7610557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7615316	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7623524	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7630130	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7631313	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7634158	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7635146	0.84[EUR][1000 genomes]
rs7641330	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7646880	0.85[EUR][1000 genomes]
rs7651071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651542	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7652687	0.91[CHD][hapmap]
rs9683085	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9808914	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9808943	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9816736	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9820353	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9820770	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9824893	0.85[EUR][1000 genomes]
rs9825207	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826786	0.86[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap]
rs9828178	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9832606	0.81[CEU][hapmap]
rs9843148	0.87[CHB][hapmap]
rs9846960	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9847364	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs9855140	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9855919	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9861997	0.91[CHB][hapmap]
rs9862919	0.90[CEU][hapmap];0.80[JPT][hapmap]
rs9866958	0.92[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs9869842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9876254	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9879995	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9882763	0.85[EUR][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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7647573	XRN1	cis	cerebellum	SCAN

Chromatin state (count:120 , 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	chr3:142233200-142251600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:142233600-142255200	Weak transcription	Fetal Stomach	stomach
22	chr3:142233600-142271000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:142237800-142251800	Weak transcription	Hela-S3	cervix
24	chr3:142238600-142269000	Weak transcription	Fetal Intestine Small	intestine
25	chr3:142239800-142269600	Weak transcription	Thymus	Thymus
26	chr3:142240800-142252400	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:142240800-142281600	Weak transcription	Fetal Brain Male	brain
28	chr3:142241000-142251600	Weak transcription	Brain Germinal Matrix	brain
29	chr3:142241000-142251600	Weak transcription	HSMMtube	muscle
30	chr3:142241000-142251800	Weak transcription	Fetal Brain Female	brain
31	chr3:142241000-142251800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:142241000-142252800	Weak transcription	Left Ventricle	heart
33	chr3:142241000-142252800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:142241000-142254600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:142241000-142280800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:142241200-142251600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:142241200-142251600	Weak transcription	Psoas Muscle	Psoas
38	chr3:142241200-142253200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:142241600-142251600	Weak transcription	Placenta	Placenta
40	chr3:142241600-142251800	Weak transcription	Fetal Lung	lung
41	chr3:142241600-142251800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:142241600-142252200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:142241800-142270800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:142242000-142251600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:142242000-142251600	Weak transcription	NH-A	brain
46	chr3:142242000-142251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:142242000-142252000	Weak transcription	HSMM	muscle
48	chr3:142242200-142251800	Weak transcription	Ovary	ovary
49	chr3:142242400-142275800	Weak transcription	NHEK	skin
50	chr3:142244400-142295600	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links