Variant report

Variant	rs7659540
Chromosome Location	chr4:153008540-153008541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12649261	0.83[ASN][1000 genomes]
rs13113320	0.85[ASN][1000 genomes]
rs4696129	0.88[ASN][1000 genomes]
rs6829453	0.91[ASN][1000 genomes]
rs6858070	0.93[ASN][1000 genomes]
rs7663766	0.83[ASN][1000 genomes]
rs7665585	0.88[ASN][1000 genomes]
rs7665985	0.88[ASN][1000 genomes]
rs7666016	0.85[CHB][hapmap]
rs7692374	0.84[ASN][1000 genomes]
rs9992635	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7659540	RP11-18H21.1	cis	Whole Blood	GTEx
rs7659540	TRIM2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152997400-153011800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:153001200-153008800	Enhancers	Thymus	Thymus
3	chr4:153002600-153010400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:153003200-153009600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr4:153003200-153013800	Enhancers	Fetal Thymus	thymus
6	chr4:153003600-153009600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr4:153003600-153014000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:153007400-153010200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr4:153007400-153010400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr4:153007600-153010200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:153007600-153010400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr4:153007600-153011800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:153007800-153009600	Weak transcription	Primary T cells from cord blood	blood
14	chr4:153007800-153010200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr4:153008000-153009200	Enhancers	Fetal Intestine Small	intestine
16	chr4:153008000-153009600	Weak transcription	Dnd41	blood
17	chr4:153008200-153015400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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Input of quick search could be:

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

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