Variant report

Variant	rs4409689
Chromosome Location	chr1:63177365-63177366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10157265	0.95[CEU][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs10159255	0.87[CEU][hapmap];0.90[CHD][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs10789117	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs10789118	0.91[CEU][hapmap]
rs10789119	0.91[CEU][hapmap];0.90[CHD][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs10789123	0.86[ASN][1000 genomes]
rs10889337	0.96[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs10889339	0.81[AMR][1000 genomes]
rs10889340	0.81[AMR][1000 genomes]
rs10889343	0.85[AMR][1000 genomes]
rs10889344	0.85[AMR][1000 genomes]
rs10889347	0.93[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs10889349	0.96[CEU][hapmap];0.83[AMR][1000 genomes]
rs10889350	0.96[CEU][hapmap];0.85[AMR][1000 genomes]
rs10889352	0.90[CEU][hapmap]
rs10889353	0.91[CEU][hapmap];0.90[CHD][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10889354	0.84[AMR][1000 genomes]
rs10889356	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10889357	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10889360	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11207981	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs11207983	0.81[AMR][1000 genomes]
rs11207984	0.80[AMR][1000 genomes]
rs11207985	0.80[AMR][1000 genomes]
rs11207986	0.80[AMR][1000 genomes]
rs11207990	0.95[CEU][hapmap];0.85[AMR][1000 genomes]
rs11207992	0.91[CEU][hapmap]
rs11207995	0.91[CEU][hapmap];0.90[CHD][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs11207997	0.83[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs11207999	0.85[AMR][1000 genomes]
rs11208000	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs11208001	0.84[AMR][1000 genomes]
rs11208004	0.91[CEU][hapmap];0.90[CHD][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs11208007	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11208009	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11485618	0.91[CEU][hapmap]
rs11577840	0.95[CEU][hapmap]
rs1168013	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes]
rs1168015	0.80[AMR][1000 genomes]
rs1168017	0.80[AMR][1000 genomes]
rs1168018	0.87[ASW][hapmap];0.95[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes]
rs1168020	0.80[AMR][1000 genomes]
rs1168021	0.80[AMR][1000 genomes]
rs1168022	0.95[CEU][hapmap]
rs1168023	0.95[CEU][hapmap]
rs1168045	0.93[ASW][hapmap];0.96[CEU][hapmap];0.90[TSI][hapmap]
rs1168085	0.81[EUR][1000 genomes]
rs1168086	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1168089	0.93[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1168093	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1168097	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1168098	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1168099	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1168102	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1168103	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1168107	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168113	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168114	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1168124	0.96[CEU][hapmap];0.86[AMR][1000 genomes]
rs1168132	0.82[CEU][hapmap];0.86[AMR][1000 genomes]
rs1179765	0.80[AMR][1000 genomes]
rs1184547	0.80[AMR][1000 genomes]
rs12025800	0.85[AMR][1000 genomes]
rs12042319	0.91[CEU][hapmap]
rs12074528	0.80[AMR][1000 genomes]
rs12090886	1.00[CEU][hapmap]
rs12116574	0.91[CEU][hapmap];0.90[CHD][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs12121288	0.86[ASN][1000 genomes]
rs12136083	0.96[CEU][hapmap];0.90[CHD][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12239736	0.84[AMR][1000 genomes]
rs12403207	0.80[AMR][1000 genomes]
rs1472257	0.85[AMR][1000 genomes]
rs1570694	0.91[CEU][hapmap];0.90[CHD][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs1627591	0.96[CEU][hapmap]
rs1629122	0.85[AMR][1000 genomes]
rs1748195	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs1748197	0.96[CEU][hapmap];0.88[AMR][1000 genomes]
rs1748199	0.93[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes]
rs1748200	0.96[CEU][hapmap];0.85[AMR][1000 genomes]
rs1748201	0.93[ASW][hapmap];0.95[CEU][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs1781195	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs1781212	0.96[CEU][hapmap]
rs1781221	0.96[CEU][hapmap]
rs2029763	0.91[CEU][hapmap]
rs2131925	0.96[CEU][hapmap];0.85[AMR][1000 genomes]
rs2131926	0.85[AMR][1000 genomes]
rs2366636	0.88[AMR][1000 genomes]
rs2366638	0.96[CEU][hapmap];0.85[AMR][1000 genomes]
rs2479464	0.87[AMR][1000 genomes]
rs3850634	0.91[CEU][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap]
rs4329540	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs4344355	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4495740	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4587594	0.91[CEU][hapmap];0.90[CHD][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes]
rs4630152	0.86[ASN][1000 genomes]
rs4915624	0.92[ASN][1000 genomes]
rs4915853	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs61471917	0.85[AMR][1000 genomes]
rs6587980	0.96[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs6657050	0.83[AMR][1000 genomes]
rs6661669	0.85[AFR][1000 genomes]
rs6664692	0.86[ASN][1000 genomes]
rs6666816	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675401	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs6678483	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs6679002	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6682423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686331	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690733	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs6693353	0.82[AMR][1000 genomes]
rs6696502	0.85[AMR][1000 genomes]
rs72915166	0.86[ASN][1000 genomes]
rs746735	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7517372	0.91[ASN][1000 genomes]
rs7518497	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7520810	0.85[AMR][1000 genomes]
rs7539035	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs7548877	0.80[AMR][1000 genomes]
rs7555577	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs880694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9659790	0.85[EUR][1000 genomes]
rs9787151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787156	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs993013	0.85[AMR][1000 genomes]
rs995000	0.91[CEU][hapmap];0.90[CHD][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]

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	nsv1014376	chr1:62976472-63181359	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4409689	DOCK7	cis	lesional skin	skin_eQTL
rs4409689	DOCK7	cis	multi-tissue	Pritchard
rs4409689	RAB11FIP2	trans	parietal	SCAN
rs4409689	DOCK7	cis	uninvolved skin	skin_eQTL
rs4409689	DOCK7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63157600-63180800	Weak transcription	Fetal Brain Male	brain
2	chr1:63163600-63186600	Weak transcription	HepG2	liver
3	chr1:63171200-63186800	Weak transcription	Fetal Stomach	stomach
4	chr1:63171400-63186400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:63172000-63186600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:63172000-63186600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:63174000-63178600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:63174000-63186800	Weak transcription	Fetal Intestine Small	intestine
9	chr1:63174600-63177600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:63176200-63177400	Weak transcription	Stomach Mucosa	stomach
11	chr1:63176800-63178000	Weak transcription	NHEK	skin

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