Variant report

Variant	rs12188594
Chromosome Location	chr5:15922387-15922388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10042283	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10520829	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10520830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11749742	0.87[CEU][hapmap];0.82[CHD][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs12186586	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188160	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517809	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12653963	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12655296	0.80[AMR][1000 genomes]
rs13153362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13154254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13164363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13185525	0.91[GIH][hapmap];0.81[LWK][hapmap];0.87[TSI][hapmap]
rs13189148	0.82[CEU][hapmap];0.82[CHB][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs146351	0.83[CEU][hapmap];0.95[MEX][hapmap]
rs1505031	0.91[CEU][hapmap];0.82[CHD][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs187705	0.83[CEU][hapmap];0.95[MEX][hapmap]
rs257734	0.87[CEU][hapmap];0.80[CHD][hapmap];0.95[MEX][hapmap]
rs257735	0.87[CEU][hapmap];0.95[MEX][hapmap]
rs257736	0.87[CEU][hapmap];0.91[MEX][hapmap]
rs257737	0.87[CEU][hapmap];0.95[MEX][hapmap]
rs257740	0.95[MEX][hapmap]
rs257741	0.87[CEU][hapmap];0.80[CHD][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs257742	0.87[CEU][hapmap];0.80[CHD][hapmap];0.91[MEX][hapmap]
rs257744	0.87[CEU][hapmap];0.80[CHD][hapmap];0.95[MEX][hapmap]
rs257745	0.91[CEU][hapmap]
rs257748	0.87[CEU][hapmap]
rs257749	0.81[CEU][hapmap]
rs257752	0.87[CEU][hapmap];0.95[MEX][hapmap]
rs257753	0.87[CEU][hapmap];0.95[MEX][hapmap]
rs257757	0.87[CEU][hapmap]
rs257758	0.87[CEU][hapmap]
rs257759	0.87[CEU][hapmap];0.95[MEX][hapmap]
rs257760	0.86[CEU][hapmap]
rs257761	0.83[CEU][hapmap];0.95[MEX][hapmap]
rs257768	0.87[CEU][hapmap];0.80[CHD][hapmap];0.95[MEX][hapmap]
rs257769	0.91[CEU][hapmap];0.80[CHD][hapmap];0.95[MEX][hapmap]
rs257772	0.82[CEU][hapmap]
rs257774	0.87[CEU][hapmap];0.95[MEX][hapmap]
rs257777	0.83[CEU][hapmap];0.95[MEX][hapmap]
rs257778	0.83[CEU][hapmap];0.95[MEX][hapmap]
rs257782	0.95[MEX][hapmap]
rs365234	0.87[CEU][hapmap];0.95[MEX][hapmap]
rs366760	0.87[CEU][hapmap]
rs389804	0.87[CEU][hapmap];0.95[MEX][hapmap]
rs3935972	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs399259	0.83[CEU][hapmap];0.86[MEX][hapmap]
rs406819	0.83[CEU][hapmap]
rs407717	0.83[CEU][hapmap];0.95[MEX][hapmap]
rs415718	0.87[CEU][hapmap];0.95[MEX][hapmap]
rs416952	0.87[CEU][hapmap];0.95[MEX][hapmap]
rs422958	0.83[CEU][hapmap];0.95[MEX][hapmap]
rs434475	0.82[CEU][hapmap]
rs4410637	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55742366	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62348083	0.81[AMR][1000 genomes]
rs6870163	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs6874587	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6876718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878591	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6878775	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6886664	0.87[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs6887439	0.88[EUR][1000 genomes]
rs6888294	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6892388	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880755	chr5:15670377-15938553	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1031483	chr5:15738485-15926083	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv461986	chr5:15854098-15943683	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv597292	chr5:15854098-15943683	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv830216	chr5:15860662-16060420	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv427712	chr5:15883439-16055856	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv4735	chr5:15916346-15961432	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12188594	MARCH11	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15913800-15936000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:15914000-15926800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:15914000-15940000	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:15914600-15928200	Weak transcription	Fetal Brain Male	brain
5	chr5:15915000-15928000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:15916600-15924800	Weak transcription	Right Ventricle	heart
7	chr5:15919000-15924600	Weak transcription	Left Ventricle	heart
8	chr5:15919000-15926800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:15919000-15926800	Weak transcription	Brain Anterior Caudate	brain
10	chr5:15919000-15926800	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:15919000-15926800	Weak transcription	Brain Substantia Nigra	brain
12	chr5:15919000-15928000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:15919000-15928200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:15919200-15928200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:15919400-15927600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:15919600-15933600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:15920000-15926600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:15920000-15933400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:15920200-15923800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:15920200-15926800	Weak transcription	Fetal Lung	lung
21	chr5:15920400-15928000	Weak transcription	Fetal Stomach	stomach
22	chr5:15922000-15923200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:15922200-15922600	Weak transcription	Ovary	ovary
24	chr5:15922200-15925000	Weak transcription	Fetal Heart	heart

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