Variant report

Variant	rs9351734
Chromosome Location	chr6:69438232-69438233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:69399809..69401625-chr6:69437402..69440315,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10806605	0.94[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap]
rs10945134	0.96[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs12194992	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12196021	0.96[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12197039	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1523931	0.94[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.86[ASN][1000 genomes]
rs1523932	0.94[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap]
rs2024561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2256337	0.87[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs2585593	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2585594	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2585618	0.87[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs2746126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746129	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2802699	0.87[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs2802705	0.87[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap]
rs28395490	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4554295	0.83[CEU][hapmap];0.91[JPT][hapmap]
rs4607402	0.91[JPT][hapmap]
rs478070	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs530888	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs639338	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455297	0.99[ASN][1000 genomes]
rs6908159	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6930275	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7753280	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9342729	0.82[JPT][hapmap]
rs9342730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9342731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9346233	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9346234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9346236	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9346237	0.83[CEU][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9346238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9351735	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9354797	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9363962	0.82[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886130	chr6:68950298-69531957	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9351734	SMAP1	cis	parietal	SCAN
rs9351734	RP3-525N10.2	cis	Whole Blood	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69435200-69439200	Enhancers	Brain Hippocampus Middle	brain
2	chr6:69435200-69439200	Enhancers	Brain Substantia Nigra	brain
3	chr6:69435400-69439200	Enhancers	Brain Cingulate Gyrus	brain
4	chr6:69436200-69439200	Enhancers	Liver	Liver
5	chr6:69436400-69439400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:69436600-69439000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:69436600-69444200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:69436800-69440200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:69437000-69438400	Weak transcription	Fetal Brain Male	brain
10	chr6:69437000-69439400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:69437200-69439000	Weak transcription	Brain Angular Gyrus	brain
12	chr6:69437200-69439200	Weak transcription	Brain Anterior Caudate	brain
13	chr6:69437800-69438600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:69438000-69438800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:69438000-69439400	Enhancers	K562	blood
16	chr6:69438000-69441000	Enhancers	Fetal Lung	lung

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