Variant report

Variant	rs2079689
Chromosome Location	chr5:12322776-12322777
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10513109	0.84[ASN][1000 genomes]
rs12657630	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12658793	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1468537	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17210105	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17210112	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17823762	0.88[AMR][1000 genomes]
rs1808270	0.87[AMR][1000 genomes]
rs2024139	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2191014	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215202	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2215253	0.87[AMR][1000 genomes]
rs2400147	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2400148	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2895923	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2907084	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2907273	0.86[AMR][1000 genomes]
rs2907278	0.85[AMR][1000 genomes]
rs2907280	0.88[AMR][1000 genomes]
rs2966901	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2966902	0.88[AMR][1000 genomes]
rs2968089	0.87[AMR][1000 genomes]
rs2968091	0.91[AMR][1000 genomes]
rs2968102	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2968103	0.88[AMR][1000 genomes]
rs2968121	0.88[AMR][1000 genomes]
rs2968122	0.87[AMR][1000 genomes]
rs32285	0.87[AMR][1000 genomes]
rs4260673	0.88[AMR][1000 genomes]
rs4702855	0.87[AMR][1000 genomes]
rs4702867	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4702869	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4702872	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4702873	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56104855	0.92[AMR][1000 genomes]
rs56236505	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59391977	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60419314	0.88[AMR][1000 genomes]
rs62338055	0.87[AMR][1000 genomes]
rs62349366	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62349369	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62349370	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62349371	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62349372	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6420013	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6871226	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6882505	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6882812	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6889543	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6890244	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6898003	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs70959019	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7735051	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs969805	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025096	chr5:12049731-12778382	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537660	chr5:12049731-12778382	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv880704	chr5:12132401-12338203	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv880364	chr5:12153033-12330841	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1030580	chr5:12254774-12364629	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1015676	chr5:12276531-12540904	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv427711	chr5:12285375-12747819	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1026529	chr5:12285675-12387812	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1017000	chr5:12285675-12451819	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv537664	chr5:12285675-12451819	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv917255	chr5:12310838-12929427	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2079689	TAS2R1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:12317400-12323800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:12320800-12323200	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr5:12321200-12322800	Enhancers	H9 Cell Line	embryonic stem cell
4	chr5:12321200-12323800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:12321400-12323400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:12321400-12323800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:12321600-12323200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr5:12321600-12323400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr5:12321600-12325800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr5:12322000-12330400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:12322200-12323400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr5:12322400-12323600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:12322400-12324200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr5:12322600-12322800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr5:12322600-12323200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr5:12322600-12324400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:12322600-12324400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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