Variant report

Variant	rs16852486
Chromosome Location	chr3:142363432-142363433
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	chr3:142360347..142363924-chr3:142363947..142367785,4	K562	blood:
2	chr3:142329516..142331316-chr3:142363067..142365225,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11715610	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.98[ASN][1000 genomes]
rs12695767	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12695768	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13058771	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13069113	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13080785	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13099848	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13100985	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1357529	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1357530	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17623267	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1916639	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1983434	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1983435	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2012010	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2030613	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2049325	0.88[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs2049326	0.80[CHB][hapmap];0.86[ASN][1000 genomes]
rs2140432	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs2177396	0.87[ASN][1000 genomes]
rs2227928	0.81[CEU][hapmap]
rs2354175	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354860	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2883380	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736560	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736561	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3922730	0.81[CEU][hapmap]
rs4413348	0.88[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs4683688	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683689	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683691	0.95[ASN][1000 genomes]
rs6440089	0.81[CEU][hapmap]
rs6440094	0.81[CEU][hapmap]
rs6440098	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6440099	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6440102	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6775813	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6782400	0.81[CEU][hapmap]
rs6783203	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6784089	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6784361	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6785894	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6789958	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6792259	0.81[CEU][hapmap]
rs6793735	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6797492	0.93[ASN][1000 genomes]
rs6798232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6799752	0.81[CEU][hapmap]
rs6802734	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6802774	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6808205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6808302	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7430429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609842	0.85[ASN][1000 genomes]
rs7610557	0.81[CEU][hapmap]
rs7615316	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7631313	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7635146	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7646880	0.98[ASN][1000 genomes]
rs7648354	1.00[CHB][hapmap];0.80[JPT][hapmap];0.95[ASN][1000 genomes]
rs7651071	0.81[CEU][hapmap]
rs940211	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940212	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816736	0.81[CEU][hapmap]
rs9824176	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9824893	0.87[ASN][1000 genomes]
rs9832606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9862919	0.85[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap]
rs9866958	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs9869842	0.81[CEU][hapmap]
rs9882763	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16852486	XRN1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142343400-142366400	Weak transcription	Fetal Intestine Small	intestine
2	chr3:142348800-142364800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:142355400-142363600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:142355400-142364000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:142357000-142371400	Weak transcription	Aorta	Aorta
6	chr3:142357600-142365200	Weak transcription	Colonic Mucosa	Colon
7	chr3:142358600-142365600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:142360800-142371400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:142362000-142363800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:142362200-142363600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:142362200-142364000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:142362400-142363600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:142362400-142363800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:142362400-142363800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:142362400-142364200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:142362400-142366800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:142362600-142363600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:142362600-142371200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:142363400-142364400	Enhancers	HepG2	liver
20	chr3:142363400-142364600	Enhancers	Liver	Liver
21	chr3:142363400-142364600	Enhancers	NHEK	skin
22	chr3:142363400-142365000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr3:142363400-142365200	Enhancers	A549	lung
24	chr3:142363400-142365200	Enhancers	HMEC	breast

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