Variant report

Variant	rs7430429
Chromosome Location	chr3:142372156-142372157
allele	C/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	MAFK	chr3:142371549-142372162	K562	blood:	n/a	chr3:142371900-142371910 chr3:142371900-142371909 chr3:142371895-142371910
2	ZNF384	chr3:142372105-142372305	K562	blood:	n/a	n/a
3	BHLHE40	chr3:142371389-142372288	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142366648..142369083-chr3:142371257..142373675,2	K562	blood:
2	chr3:142369264..142373195-chr3:142384252..142386650,3	K562	blood:

Variant related genes	Relation type
PLS1	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

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];0.85[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.98[ASN][1000 genomes]
rs12695767	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12695768	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13058771	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13069113	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13080785	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13099848	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13100985	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1357529	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1357530	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16852486	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]
rs17623267	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1916639	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1983434	0.80[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1983435	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2012010	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2030613	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2049325	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]
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[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2177396	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2227928	0.81[CEU][hapmap]
rs2354175	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354860	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2883380	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];0.99[ASN][1000 genomes]
rs3736560	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736561	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[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[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs4683688	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683689	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[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	0.80[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6440099	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6440102	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6770411	0.88[YRI][hapmap]
rs6775813	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6782400	0.81[CEU][hapmap]
rs6783203	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6784089	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6784361	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6785894	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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];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]
rs6797492	0.93[ASN][1000 genomes]
rs6798232	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[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	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6808205	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]
rs6808302	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7631313	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7635146	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7646880	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7648354	1.00[CHB][hapmap];0.80[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7651071	0.81[CEU][hapmap]
rs940211	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940212	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[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	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9832606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.98[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	0.80[AMR][1000 genomes];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7430429	XRN1	cis	cerebellum	SCAN
rs7430429	PLS1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142367800-142375400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:142367800-142375400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:142369200-142379200	Weak transcription	Dnd41	blood
5	chr3:142369400-142408400	Weak transcription	Pancreas	Pancrea
6	chr3:142369600-142375800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:142370200-142372600	Strong transcription	Fetal Intestine Small	intestine
8	chr3:142370800-142372200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:142371000-142393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:142371200-142372800	Enhancers	A549	lung
11	chr3:142371400-142372200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:142371400-142372400	Enhancers	Ovary	ovary
13	chr3:142371600-142372200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:142371600-142372400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:142371800-142372200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr3:142371800-142372200	Flanking Active TSS	K562	blood
17	chr3:142372000-142372200	Enhancers	Liver	Liver
18	chr3:142372000-142375800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:142372000-142382000	Weak transcription	HepG2	liver
20	chr3:142372000-142382800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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