Variant report

Variant	rs1349777
Chromosome Location	chr11:59194315-59194316
allele	A/C
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	JUND	chr11:59193729-59194795	H1-hESC	embryonic stem cell:	n/a	chr11:59194444-59194453

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:59191985..59194660-chr11:59317769..59320610,2	K562	blood:

Variant related genes	Relation type
OR5A2	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1026320	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229957	0.85[EUR][1000 genomes]
rs11229958	0.85[EUR][1000 genomes]
rs11601772	0.81[CEU][hapmap]
rs11602535	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11602856	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11604452	0.88[TSI][hapmap]
rs11605288	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11605572	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11606927	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11606980	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12417674	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12418613	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12419033	0.84[EUR][1000 genomes]
rs12419445	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12420159	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12420443	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12420477	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12785234	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12787182	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12801196	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12806497	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12808401	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12808731	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1453541	0.86[TSI][hapmap]
rs1453542	0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs1453544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1453547	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1453549	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1453550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1453551	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1453552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1522759	0.87[TSI][hapmap]
rs1589601	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1608210	0.85[EUR][1000 genomes]
rs1608211	0.85[EUR][1000 genomes]
rs17498652	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17500478	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17584022	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17591107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1901856	0.85[EUR][1000 genomes]
rs1955070	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2040326	0.82[TSI][hapmap]
rs2167923	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2198451	0.87[EUR][1000 genomes]
rs34037092	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34387009	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34730029	0.84[EUR][1000 genomes]
rs35630700	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35872497	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4938916	0.87[TSI][hapmap]
rs4939291	0.85[EUR][1000 genomes]
rs61901576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61901620	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61902489	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61902558	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61904569	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61904597	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6591536	0.81[TSI][hapmap]
rs7105556	0.82[TSI][hapmap]
rs7121582	0.84[TSI][hapmap]
rs7929008	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7934882	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7935959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7952071	0.84[EUR][1000 genomes]
rs9787928	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1046084	chr11:59034871-59314519	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1047952	chr11:59124719-59221606	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1349777	DDB1	cis	parietal	SCAN
rs1349777	OR5AR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59191600-59194600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:59192400-59194800	Enhancers	H9 Cell Line	embryonic stem cell
3	chr11:59192800-59194600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:59192800-59194800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr11:59193000-59194800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr11:59193200-59194400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:59193200-59194600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:59193200-59195600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:59193400-59195000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr11:59193600-59194400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr11:59193600-59194400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr11:59193600-59194400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr11:59193600-59194600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr11:59193600-59194600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr11:59193800-59194600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr11:59194000-59194600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:59194000-59194800	Enhancers	Stomach Mucosa	stomach
18	chr11:59194000-59195200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr11:59194200-59194400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:59194200-59194600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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