Variant report

Variant	rs6793735
Chromosome Location	chr3:142408606-142408607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11715610	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12695767	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12695768	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13058771	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13069113	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13079246	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13080785	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13099848	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13100985	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1357529	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1357530	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16852486	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]
rs17623267	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1916639	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1983434	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1983435	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2012010	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2030613	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2049325	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]
rs2049326	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2140432	0.88[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2177396	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2227928	0.81[CEU][hapmap]
rs2354175	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2354860	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2883380	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];0.95[ASN][1000 genomes]
rs3736560	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736561	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4413348	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]
rs4683688	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683689	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683690	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683691	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6440089	0.81[CEU][hapmap]
rs6440094	0.81[CEU][hapmap]
rs6440098	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6440099	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6440102	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6775813	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6782400	0.81[CEU][hapmap]
rs6783203	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6784089	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6784361	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6785894	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6789958	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6792259	0.81[CEU][hapmap]
rs6797492	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6798232	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6799752	0.81[CEU][hapmap]
rs6802734	0.94[ASN][1000 genomes]
rs6802774	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6808205	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]
rs6808302	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7430429	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7609842	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7610557	0.81[CEU][hapmap]
rs7615316	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7631313	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7635146	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7646880	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7648354	0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7651071	0.81[CEU][hapmap]
rs940211	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs940212	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9824176	0.82[ASN][1000 genomes]
rs9824893	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9832606	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862919	0.85[CEU][hapmap];0.84[CHB][hapmap]
rs9866958	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9869842	0.81[CEU][hapmap]
rs9882763	0.87[AMR][1000 genomes];0.83[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6793735	XRN1	cis	cerebellum	SCAN
rs6793735	PLS1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142379200-142413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:142384400-142411400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:142385800-142415400	Weak transcription	A549	lung
5	chr3:142386400-142411800	Weak transcription	NHEK	skin
6	chr3:142387400-142413400	Weak transcription	Stomach Mucosa	stomach
7	chr3:142389200-142412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:142389200-142414800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:142389400-142408800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:142389400-142410000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:142389800-142442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:142392600-142410200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:142392800-142418000	Weak transcription	HepG2	liver
14	chr3:142392800-142425400	Weak transcription	Dnd41	blood
15	chr3:142392800-142433000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:142393000-142426000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:142393400-142426200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:142401200-142410000	Weak transcription	Primary T cells from cord blood	blood
19	chr3:142402400-142408800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr3:142403000-142412800	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr3:142404200-142418000	Weak transcription	HMEC	breast
22	chr3:142404600-142416200	Weak transcription	Fetal Intestine Small	intestine
23	chr3:142405800-142411600	Weak transcription	Fetal Intestine Large	intestine
24	chr3:142406800-142408800	Strong transcription	Liver	Liver
25	chr3:142407000-142410600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr3:142407200-142417000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:142407400-142409000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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