Variant report

Variant	rs7516230
Chromosome Location	chr1:224210867-224210868
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10799413	0.82[AMR][1000 genomes]
rs10916149	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10916170	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12027895	0.88[CEU][hapmap]
rs12079350	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12121620	0.80[EUR][1000 genomes]
rs12562321	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs2404851	0.84[EUR][1000 genomes]
rs3933010	0.81[AMR][1000 genomes]
rs4601554	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4653912	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55772500	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59220538	0.87[EUR][1000 genomes]
rs59305941	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61823340	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv873216	chr1:224075483-224230307	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic 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	27 gene(s)	inside rSNPs	diseases
5	nsv873219	chr1:224097155-224216822	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv873220	chr1:224097155-224223659	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv549241	chr1:224103992-224216757	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv549243	chr1:224115297-224216757	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv549248	chr1:224183599-224216757	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv549249	chr1:224183599-224216822	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv1847784	chr1:224185036-224227122	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv1795476	chr1:224186148-224226044	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv549252	chr1:224201825-224216757	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv549256	chr1:224201927-224216757	ZNF genes & repeats Enhancers Weak transcription Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv16231	chr1:224204343-224241314	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats 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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7516230	RP11-504P24.4	cis	Thyroid	GTEx
rs7516230	RP11-504P24.3	cis	Nerve Tibial	GTEx
rs7516230	TP53BP2	cis	lymphoblastoid	seeQTL
rs7516230	RP11-504P24.6	cis	Thyroid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224210600-224214400	Weak transcription	NHDF-Ad	bronchial
2	chr1:224210800-224211000	Enhancers	Ovary	ovary

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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