Variant report

Variant	rs6808205
Chromosome Location	chr3:142365769-142365770
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142343680..142345636-chr3:142364474..142366774,2	K562	blood:
2	chr3:142360347..142363924-chr3:142363947..142367785,4	K562	blood:
3	chr3:142344136..142346877-chr3:142364474..142366213,2	K562	blood:
4	chr3:142358804..142361847-chr3:142364115..142367127,3	K562	blood:
5	chr3:142361260..142362902-chr3:142365127..142366866,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11715610	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs12695767	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12695768	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13058771	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13069113	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13080785	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13099848	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13100985	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1357529	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1357530	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16852486	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]
rs17623267	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1916639	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1983434	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1983435	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2012010	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2030613	0.88[CEU][hapmap];0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2049325	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]
rs2049326	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs2140432	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2177396	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2227928	0.81[CEU][hapmap]
rs2354175	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2354860	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2883380	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];0.96[ASN][1000 genomes]
rs3736560	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736561	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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];0.84[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs4683688	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683689	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683691	0.93[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];0.90[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6440099	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6440102	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770411	0.81[YRI][hapmap]
rs6775813	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6782400	0.81[CEU][hapmap]
rs6783203	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6784089	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6784361	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6785894	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6789958	1.00[CEU][hapmap];0.89[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];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6797492	0.91[ASN][1000 genomes]
rs6798232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799752	0.81[CEU][hapmap]
rs6802734	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6802774	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6808302	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7430429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7609842	0.83[ASN][1000 genomes]
rs7610557	0.81[CEU][hapmap]
rs7615316	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7631313	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7635146	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7646880	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7648354	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7651071	0.81[CEU][hapmap]
rs940211	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs940212	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9816736	0.81[CEU][hapmap]
rs9824176	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9824893	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9832606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9862919	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs9866958	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs9869842	0.81[CEU][hapmap]
rs9882763	0.80[AMR][1000 genomes];0.84[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
rs6808205	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	chr3:142357000-142371400	Weak transcription	Aorta	Aorta
3	chr3:142360800-142371400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:142362400-142366800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:142362600-142371200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:142363600-142365800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:142363600-142367200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:142364200-142367800	Enhancers	Stomach Mucosa	stomach
9	chr3:142364400-142371800	Weak transcription	HepG2	liver
10	chr3:142364600-142368400	Weak transcription	Liver	Liver
11	chr3:142364800-142365800	Genic enhancers	Rectal Mucosa Donor 29	rectum
12	chr3:142364800-142369400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:142365000-142369000	Weak transcription	NH-A	brain
14	chr3:142365000-142371600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:142365200-142366000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:142365200-142366000	Enhancers	Colonic Mucosa	Colon
17	chr3:142365200-142366600	Weak transcription	A549	lung
18	chr3:142365400-142367200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:142365600-142367200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:142365600-142367400	Enhancers	HMEC	breast
21	chr3:142365600-142367400	Enhancers	NHEK	skin
22	chr3:142365600-142367800	Enhancers	Duodenum Mucosa	Duodenum
23	chr3:142365600-142369200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:142365600-142369400	Enhancers	Rectal Mucosa Donor 31	rectum

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