Variant report

Variant	rs11629899
Chromosome Location	chr15:33220987-33220988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10152541	1.00[JPT][hapmap]
rs10519764	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10519765	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11629687	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11631608	0.91[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11632728	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11632769	0.82[CEU][hapmap]
rs11633201	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs11633554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11634576	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs11635920	0.87[ASW][hapmap];0.91[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11635965	0.91[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11637646	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12708498	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs12899881	0.91[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12904054	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12904870	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs12905485	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12909023	0.95[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12913108	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13379651	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1376791	0.86[CEU][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap]
rs16961209	0.87[ASW][hapmap];0.95[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17228929	0.82[CEU][hapmap]
rs17228971	0.96[ASN][1000 genomes]
rs17816519	0.91[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17816555	0.95[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1993132	0.86[ASN][1000 genomes]
rs1993133	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs2122436	0.83[CEU][hapmap]
rs2339163	0.95[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2339164	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs347915	0.84[CEU][hapmap]
rs347921	0.81[CEU][hapmap]
rs347951	0.81[CEU][hapmap]
rs347952	0.84[CEU][hapmap]
rs35639096	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35937803	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36100673	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812926	0.95[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs43768	0.84[CEU][hapmap]
rs62003760	0.86[ASN][1000 genomes]
rs68110693	0.92[AMR][1000 genomes]
rs7178559	0.83[EUR][1000 genomes]
rs72719313	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9806422	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9806436	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv832962	chr15:33111517-33239736	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv903978	chr15:33144202-33308641	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv903980	chr15:33149087-33264201	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv568917	chr15:33167171-33304172	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11629899	GABRA5	cis	parietal	SCAN
rs11629899	FAN1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33202600-33224600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:33215200-33221200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr15:33215600-33221000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:33216200-33234800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:33216400-33227200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr15:33216800-33221000	Weak transcription	Osteobl	bone
7	chr15:33217000-33229400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:33219400-33221400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:33220800-33221600	Enhancers	HUES48 Cell Line	embryonic stem cell

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