Variant report

Variant	rs2049325
Chromosome Location	chr3:142337430-142337431
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr3:142337396-142338406	K562	blood:	n/a	n/a
2	FOXA2	chr3:142337208-142338321	A549	lung:	n/a	chr3:142338143-142338155
3	FOXA2	chr3:142337045-142338374	A549	lung:	n/a	chr3:142337064-142337076 chr3:142338143-142338155
4	GATA1	chr3:142337277-142338381	K562	blood:	n/a	n/a
5	RCOR1	chr3:142337423-142338247	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142337305..142339939-chr3:142351079..142353328,2	K562	blood:
2	chr3:142336507..142339486-chr3:142355322..142357574,2	MCF-7	breast:
3	chr3:142327574..142330140-chr3:142335677..142337995,2	MCF-7	breast:
4	chr3:142294824..142296664-chr3:142335818..142337448,2	K562	blood:
5	chr3:142336924..142339246-chr3:142443118..142445487,2	MCF-7	breast:

Variant related genes	Relation type
PLS1	TF binding region
ENSG00000144935	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10935465	0.86[EUR][1000 genomes]
rs1129393	0.86[EUR][1000 genomes]
rs11715610	0.90[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12695767	0.83[ASN][1000 genomes]
rs12695768	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13058771	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13065075	0.82[EUR][1000 genomes]
rs13067795	0.84[EUR][1000 genomes]
rs13069113	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13069307	0.82[EUR][1000 genomes]
rs13079246	0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13080785	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13085998	0.85[EUR][1000 genomes]
rs13093869	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13099848	0.80[ASN][1000 genomes]
rs13100985	0.85[ASN][1000 genomes]
rs1357529	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1357530	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16852486	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]
rs17623267	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1916639	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1983434	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1983435	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2012010	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2030613	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2049326	0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140432	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2177396	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227928	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2227930	0.86[EUR][1000 genomes]
rs2354175	0.86[ASN][1000 genomes]
rs2354860	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2883380	0.88[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs3736560	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3736561	0.85[ASN][1000 genomes]
rs3922730	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs4413348	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683688	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4683689	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4683690	0.88[CEU][hapmap];0.90[CHB][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4683691	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6414350	0.83[EUR][1000 genomes]
rs6440088	0.86[EUR][1000 genomes]
rs6440089	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs6440090	0.92[EUR][1000 genomes]
rs6440091	0.89[EUR][1000 genomes]
rs6440092	0.91[EUR][1000 genomes]
rs6440093	0.92[EUR][1000 genomes]
rs6440094	0.92[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs6440098	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440099	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6440102	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6768093	0.87[EUR][1000 genomes]
rs6770155	0.92[EUR][1000 genomes]
rs6775813	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6780250	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs6782400	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs6783203	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6784089	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6784361	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6785894	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6789958	0.88[CEU][hapmap]
rs6792259	0.92[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs6793735	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6798232	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs6799752	0.92[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs6802734	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6802774	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6808205	0.88[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs6808302	0.84[ASN][1000 genomes]
rs7428496	0.88[EUR][1000 genomes]
rs7430429	0.88[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs7609842	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610557	0.92[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs7615316	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7631313	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7635146	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7641330	0.82[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs7646880	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7647573	0.85[EUR][1000 genomes]
rs7648354	0.89[CHB][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7651071	0.92[CEU][hapmap]
rs7651542	0.84[EUR][1000 genomes]
rs940211	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs940212	0.86[ASN][1000 genomes]
rs9683085	0.85[EUR][1000 genomes]
rs9816736	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap]
rs9824176	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9824893	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9825207	0.87[EUR][1000 genomes]
rs9832606	0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9846960	0.81[CEU][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs9862919	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9866958	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9869842	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs9879995	0.87[EUR][1000 genomes]
rs9882763	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
rs2049325	XRN1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142317200-142337600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:142317400-142337800	Weak transcription	HepG2	liver
3	chr3:142333200-142337600	Weak transcription	HMEC	breast
4	chr3:142333200-142337600	Weak transcription	NHEK	skin
5	chr3:142334000-142357200	Weak transcription	Pancreas	Pancrea
6	chr3:142334200-142337800	Weak transcription	Fetal Brain Male	brain
7	chr3:142335400-142338400	Enhancers	Fetal Intestine Small	intestine
8	chr3:142336000-142339400	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr3:142336000-142340800	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr3:142336600-142338000	Enhancers	Fetal Intestine Large	intestine
11	chr3:142337000-142337600	Enhancers	Small Intestine	intestine
12	chr3:142337000-142337600	Enhancers	K562	blood
13	chr3:142337000-142338000	Enhancers	Colonic Mucosa	Colon
14	chr3:142337000-142338400	Enhancers	Duodenum Mucosa	Duodenum
15	chr3:142337200-142338800	Flanking Active TSS	A549	lung
16	chr3:142337400-142337600	Flanking Active TSS	Stomach Mucosa	stomach
17	chr3:142337400-142337800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr3:142337400-142337800	Enhancers	Gastric	stomach
19	chr3:142337400-142338000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr3:142337400-142338000	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr3:142337400-142338600	Enhancers	HUVEC	blood vessel

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