Variant report

Variant	rs4681746
Chromosome Location	chr3:56733384-56733385
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56715683..56718669-chr3:56731865..56734737,3	K562	blood:
2	chr3:56716874..56719252-chr3:56732973..56734497,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1045926	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs10865999	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs11130536	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11130538	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11706624	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs11712256	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712278	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715395	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs11719656	0.80[ASN][1000 genomes]
rs12488218	0.80[ASN][1000 genomes]
rs12493637	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13097030	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs1491166	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1565374	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1602190	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17056878	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs2004199	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2029464	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2029465	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2054987	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs2054988	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs2291499	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs2291501	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2317133	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs35998149	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4681951	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4681963	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs66529035	0.80[ASN][1000 genomes]
rs7432897	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7612599	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs7618024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9811046	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs9820759	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9841915	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842283	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9858728	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9862490	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9881005	0.95[CHB][hapmap];0.96[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	nsv237149	chr3:56732922-56738481	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4681746	CCDC66	cis	Thyroid	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56725800-56734000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:56726000-56734000	Weak transcription	NHEK	skin
3	chr3:56729800-56738600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:56730000-56738600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr3:56730400-56738600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:56731000-56736400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:56731000-56736400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:56731000-56736400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:56731000-56736800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:56731000-56736800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:56731200-56734000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:56731200-56734200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:56731200-56736400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:56731200-56736400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:56731200-56738600	Weak transcription	Primary T cells from cord blood	blood
16	chr3:56731200-56738600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:56731200-56738600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:56733000-56733400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr3:56733000-56734000	Enhancers	Placenta	Placenta

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