Variant report

Variant	rs1368341
Chromosome Location	chr5:145116796-145116797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10035959	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10035998	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10038598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10041421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1019922	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1019923	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1019925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1019926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1025472	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11956768	1.00[JPT][hapmap]
rs12518852	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13166750	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13169344	0.80[EUR][1000 genomes]
rs1347123	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1347124	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1368340	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1368342	0.80[EUR][1000 genomes]
rs1368343	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432753	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1433028	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1529708	0.81[ASN][1000 genomes]
rs1619551	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1626062	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1626734	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1654133	0.87[EUR][1000 genomes]
rs1654134	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1654135	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1654143	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1654144	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1654145	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1654146	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1654147	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1654148	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1654150	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1654230	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1654231	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1654232	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1654233	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1654234	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1654235	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1654236	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1654237	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1654238	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1654239	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1654240	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1654242	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1654243	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1821250	0.87[MEX][hapmap]
rs1835931	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1897540	0.83[ASN][1000 genomes]
rs1897542	0.80[EUR][1000 genomes]
rs1962863	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1962864	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1972777	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1972778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2014625	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2278378	1.00[JPT][hapmap]
rs2400196	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2400197	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2400198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2400199	0.88[EUR][1000 genomes]
rs2436416	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs338884	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs338887	0.85[CEU][hapmap];0.80[TSI][hapmap]
rs338889	0.85[CEU][hapmap]
rs338894	0.87[MEX][hapmap]
rs338895	0.85[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap]
rs338896	0.85[CEU][hapmap];0.80[TSI][hapmap]
rs338897	0.85[CEU][hapmap];0.80[TSI][hapmap]
rs3903516	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4305683	0.94[MEX][hapmap]
rs4521541	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580383	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580384	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867440	0.81[TSI][hapmap]
rs6884968	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896903	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721955	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs872565	0.83[ASN][1000 genomes]
rs872566	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs987806	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs998158	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462474	chr5:145068001-145143775	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv599934	chr5:145068001-145143775	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1021851	chr5:145106686-145187560	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1368341	SPINK5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145101600-145117400	Weak transcription	Gastric	stomach
2	chr5:145105400-145179000	Weak transcription	Pancreas	Pancrea
3	chr5:145107200-145123200	Weak transcription	Aorta	Aorta
4	chr5:145109400-145120600	Weak transcription	Left Ventricle	heart
5	chr5:145109400-145194400	Weak transcription	Colonic Mucosa	Colon
6	chr5:145109600-145116800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:145110400-145143800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:145111200-145123000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:145111400-145166800	Weak transcription	K562	blood
10	chr5:145113000-145117400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:145113600-145140000	Weak transcription	Ovary	ovary
12	chr5:145113800-145118800	Weak transcription	Fetal Intestine Small	intestine
13	chr5:145114000-145117400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:145114000-145163400	Weak transcription	Small Intestine	intestine
15	chr5:145114200-145117800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:145114600-145142400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr5:145114800-145139200	Weak transcription	Fetal Intestine Large	intestine
18	chr5:145115200-145117000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr5:145115800-145143800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr5:145116400-145123200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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