Variant report

Variant	rs7614952
Chromosome Location	chr3:45900621-45900622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:45893387..45895518-chr3:45899980..45902424,2	K562	blood:
2	chr3:45900001..45902515-chr3:45903803..45908425,6	K562	blood:
3	chr3:45882084..45884480-chr3:45897163..45900621,3	K562	blood:
4	chr3:45900221..45902681-chr3:45909475..45912786,3	K562	blood:

Variant related genes	Relation type
ENSG00000163818	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1029732	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1058961	0.90[CHB][hapmap]
rs1125823	0.80[ASN][1000 genomes]
rs11916880	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13065964	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs1386930	0.86[CHB][hapmap]
rs1488369	0.86[CHB][hapmap]
rs57667195	0.90[ASN][1000 genomes]
rs59647542	0.85[ASN][1000 genomes]
rs62245073	0.88[ASN][1000 genomes]
rs62245074	0.88[ASN][1000 genomes]
rs62245076	0.90[ASN][1000 genomes]
rs73830464	0.87[ASN][1000 genomes]
rs7625839	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs952287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9855780	0.80[ASN][1000 genomes]
rs9856760	0.84[YRI][hapmap];0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7614952	SLC6A20	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45890000-45907400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:45891800-45905200	Weak transcription	Psoas Muscle	Psoas
3	chr3:45894600-45906200	Genic enhancers	Dnd41	blood
4	chr3:45894800-45900800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:45895600-45902200	Weak transcription	Primary T cells from cord blood	blood
6	chr3:45896600-45902600	Weak transcription	Thymus	Thymus
7	chr3:45898200-45902400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:45898400-45902200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:45899200-45902800	Enhancers	Liver	Liver
10	chr3:45900200-45901000	Enhancers	Primary B cells from cord blood	blood
11	chr3:45900200-45901000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr3:45900200-45901000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:45900400-45900800	Enhancers	Duodenum Mucosa	Duodenum
14	chr3:45900400-45901000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:45900400-45901000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:45900400-45901000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:45900400-45901000	Enhancers	Fetal Thymus	thymus
18	chr3:45900400-45901200	Enhancers	Primary hematopoietic stem cells	blood
19	chr3:45900400-45901400	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:45900400-45902200	Enhancers	GM12878-XiMat	blood
21	chr3:45900600-45900800	Enhancers	K562	blood
22	chr3:45900600-45901600	Weak transcription	Fetal Intestine Small	intestine
23	chr3:45900600-45902200	Weak transcription	Stomach Mucosa	stomach

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