Variant report

Variant	rs7259178
Chromosome Location	chr19:21616595-21616596
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21614539..21617498-chr19:21618431..21621735,3	K562	blood:

Extended variants
information (count: 120 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1012040	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10406824	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11085455	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12150996	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12151067	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12151068	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12151222	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12971724	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12975330	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12975981	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12976011	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12981869	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12984238	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1500400	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1500401	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1520073	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1533675	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1566474	0.83[ASN][1000 genomes]
rs1566476	0.83[ASN][1000 genomes]
rs1566477	0.83[ASN][1000 genomes]
rs1607664	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1678822	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs16997799	0.85[YRI][hapmap]
rs16997924	0.83[ASN][1000 genomes]
rs17618715	1.00[JPT][hapmap]
rs17618778	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1813234	0.85[CEU][hapmap]
rs1984771	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2133816	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2133820	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2173724	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2246914	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2262897	0.83[ASN][1000 genomes]
rs2358984	0.86[CEU][hapmap]
rs2562399	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2562448	1.00[JPT][hapmap]
rs2562457	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2562458	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2562459	0.83[ASN][1000 genomes]
rs2650774	0.83[AFR][1000 genomes]
rs2650775	0.83[EUR][1000 genomes]
rs2650778	0.83[ASN][1000 genomes]
rs2650779	1.00[JPT][hapmap]
rs2650780	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2650781	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2650782	0.83[ASN][1000 genomes]
rs2650783	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2650785	0.83[ASN][1000 genomes]
rs2650786	0.83[ASN][1000 genomes]
rs2650791	1.00[JPT][hapmap]
rs2650794	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2650799	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2650808	0.83[ASN][1000 genomes]
rs2650845	1.00[CEU][hapmap]
rs2681371	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2681372	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs28839521	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2914636	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs2914647	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2914648	0.85[AFR][1000 genomes]
rs2914649	0.83[AFR][1000 genomes]
rs2937158	0.85[AFR][1000 genomes]
rs2937159	0.85[AFR][1000 genomes]
rs2937161	0.83[EUR][1000 genomes]
rs2968081	0.83[ASN][1000 genomes]
rs2968084	0.85[AFR][1000 genomes]
rs34560125	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34875588	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35148123	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35245030	0.83[ASN][1000 genomes]
rs35578515	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35860067	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4332859	0.83[ASN][1000 genomes]
rs4341872	1.00[CEU][hapmap]
rs488125	0.85[CEU][hapmap]
rs501647	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs504280	0.81[CEU][hapmap]
rs509540	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs56152627	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs566230	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs57841525	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62110379	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62111469	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62111470	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62111472	0.83[ASN][1000 genomes]
rs62111476	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6511247	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs669046	1.00[JPT][hapmap]
rs67723811	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs685844	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs7246684	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7249636	0.85[CEU][hapmap]
rs7257584	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7258211	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7258523	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8100318	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs8101077	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8101442	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8102252	0.81[AFR][1000 genomes]
rs8102655	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8102854	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs8103151	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8105404	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8105629	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107042	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8107940	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8107999	0.82[CHB][hapmap]
rs8110230	0.82[EUR][1000 genomes]
rs8111189	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs8112359	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8113558	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs880896	0.82[CHB][hapmap]
rs939301	0.82[CHB][hapmap]

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	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
5	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7259178	ZNF429,LOC400680	cis	thalamus	BrainEAC
rs7259178	ZNF429,LOC400680	cis	brain	BrainEAC
rs7259178	ZNF738	cis	Esophagus Muscularis	GTEx
rs7259178	ZNF429,LOC400680	cis	frontal cortex	BrainEAC
rs7259178	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs7259178	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs7259178	ZNF429,LOC400680	cis	hippocampus	BrainEAC
rs7259178	ZNF429	cis	Whole Blood	GTEx
rs7259178	ZNF429,LOC400680	cis	temporal cortex	BrainEAC

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21607600-21630200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:21613400-21618600	ZNF genes & repeats	Liver	Liver
3	chr19:21616400-21616600	Weak transcription	Pancreas	Pancrea

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