Variant report

Variant	rs4146556
Chromosome Location	chr5:15735956-15735957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10866514	0.80[CHD][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes]
rs11133821	0.87[AMR][1000 genomes]
rs11748700	0.80[LWK][hapmap]
rs11748790	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11750054	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11951416	1.00[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes]
rs12152734	0.89[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12153463	0.89[AMR][1000 genomes]
rs12153747	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12519807	0.85[YRI][hapmap]
rs12659413	0.82[YRI][hapmap]
rs13180702	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13358928	0.83[CEU][hapmap];0.81[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16867538	0.85[CHB][hapmap];0.90[CHD][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16867615	0.86[CHB][hapmap]
rs16867617	0.86[CHB][hapmap];0.85[LWK][hapmap];0.81[TSI][hapmap]
rs17602470	0.81[ASN][1000 genomes]
rs2937073	0.81[AMR][1000 genomes]
rs2937074	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2937075	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34308971	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35167698	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35719201	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4133004	0.81[JPT][hapmap]
rs4235554	0.86[CHB][hapmap];0.85[LWK][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap]
rs4235555	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4273602	0.82[YRI][hapmap]
rs4273604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4289558	0.80[LWK][hapmap];0.83[YRI][hapmap];0.80[ASN][1000 genomes]
rs4293917	0.93[YRI][hapmap]
rs4312881	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4318779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4320259	0.83[YRI][hapmap]
rs4330464	0.80[ASN][1000 genomes]
rs4484432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4568364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4574543	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4576146	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4582274	0.83[YRI][hapmap];0.80[ASN][1000 genomes]
rs4701638	0.88[AMR][1000 genomes]
rs4701639	0.89[CEU][hapmap];0.92[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4701641	0.89[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4702102	0.89[CEU][hapmap];0.93[CHB][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4702103	0.86[CHB][hapmap];0.81[TSI][hapmap]
rs4702108	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6554897	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6862949	0.88[AMR][1000 genomes]
rs6892021	0.89[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6892414	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7709102	0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7713555	0.85[YRI][hapmap]
rs924455	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv830214	chr5:15589809-15791032	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3507774	chr5:15593461-15822407	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3507776	chr5:15593461-15822407	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1028089	chr5:15636285-15883910	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv537676	chr5:15636285-15883910	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1024248	chr5:15638067-15863583	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv537677	chr5:15638067-15863583	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv880755	chr5:15670377-15938553	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
13	esv2757107	chr5:15678556-15810987	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv2759327	chr5:15678556-15810987	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv2763894	chr5:15714022-15863332	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4146556	SLC23A3	trans	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15728400-15737000	Weak transcription	NHDF-Ad	bronchial
2	chr5:15731200-15746000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:15732000-15745800	Weak transcription	Right Atrium	heart
4	chr5:15732200-15736800	Weak transcription	Right Ventricle	heart
5	chr5:15732200-15737800	Weak transcription	Aorta	Aorta
6	chr5:15732400-15737000	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:15732800-15737000	Weak transcription	Brain Substantia Nigra	brain
8	chr5:15733000-15737000	Weak transcription	Brain Hippocampus Middle	brain
9	chr5:15734000-15737000	Enhancers	Fetal Heart	heart
10	chr5:15734400-15738000	Weak transcription	Ovary	ovary
11	chr5:15734600-15738800	Weak transcription	Left Ventricle	heart
12	chr5:15734600-15739200	Weak transcription	Lung	lung
13	chr5:15734800-15737000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:15735800-15736000	Enhancers	Fetal Brain Male	brain

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