Variant report

Variant	rs6445814
Chromosome Location	chr3:56727885-56727886
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:56708568..56710932-chr3:56727678..56729297,2	MCF-7	breast:
2	chr3:56715572..56717883-chr3:56727378..56729582,3	MCF-7	breast:
3	chr3:56726200..56728005-chr3:56842796..56845095,2	MCF-7	breast:
4	chr3:56716408..56719347-chr3:56726422..56729753,3	K562	blood:

Variant related genes	Relation type
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10049468	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11130537	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130540	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130541	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1565373	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1565375	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17235670	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2317134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs2317244	0.85[EUR][1000 genomes]
rs2317252	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs282522	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap]
rs4234393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4681734	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681740	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4681945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4681964	0.86[EUR][1000 genomes]
rs4681980	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4681994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4682000	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62251242	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445801	0.81[EUR][1000 genomes]
rs6445803	0.86[EUR][1000 genomes]
rs6445804	0.84[EUR][1000 genomes]
rs6445810	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6781293	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap]
rs6787227	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6792321	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6802498	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6809499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73079863	0.80[AFR][1000 genomes]
rs7618007	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7619465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7620259	0.85[EUR][1000 genomes]
rs7631662	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7637449	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs7642389	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9311614	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs958755	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs9809309	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9833926	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs9835332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9839065	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9851653	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858568	0.84[EUR][1000 genomes]
rs9875257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9878373	0.86[EUR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6445814	CCDC66	cis	Thyroid	GTEx
rs6445814	CCDC66	cis	cerebellum	SCAN
rs6445814	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL
rs6445814	CCDC66	cis	lymphoblastoid	seeQTL
rs6445814	ARHGEF3	cis	cerebellum	SCAN
rs6445814	CHDH	cis	cerebellum	SCAN

Chromatin state (count:43 , 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	chr3:56726200-56729200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:56726400-56729800	Enhancers	Fetal Thymus	thymus
5	chr3:56726600-56729600	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:56726600-56730000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:56726800-56728000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr3:56726800-56728000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:56726800-56728000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:56726800-56728200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr3:56726800-56728200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:56726800-56729600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr3:56726800-56729600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:56727000-56728000	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr3:56727000-56728000	Enhancers	HSMM	muscle
16	chr3:56727000-56728200	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr3:56727000-56728200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr3:56727000-56729600	Enhancers	Primary hematopoietic stem cells	blood
19	chr3:56727200-56728000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:56727200-56729600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:56727200-56729800	Enhancers	Thymus	Thymus
22	chr3:56727200-56730000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:56727400-56728000	Enhancers	HSMMtube	muscle
24	chr3:56727400-56728200	Enhancers	Duodenum Mucosa	Duodenum
25	chr3:56727400-56728400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr3:56727600-56728000	Enhancers	Dnd41	blood
27	chr3:56727600-56728200	Enhancers	HUVEC	blood vessel
28	chr3:56727600-56729600	Enhancers	Primary B cells from cord blood	blood
29	chr3:56727600-56729600	Enhancers	GM12878-XiMat	blood
30	chr3:56727600-56729800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr3:56727600-56730000	Enhancers	Primary T cells fromperipheralblood	blood
32	chr3:56727600-56730400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:56727600-56731000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr3:56727600-56731200	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr3:56727600-56731200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr3:56727800-56728000	Enhancers	Placenta	Placenta
37	chr3:56727800-56728000	Enhancers	Hela-S3	cervix
38	chr3:56727800-56728200	Enhancers	Adipose Nuclei	Adipose
39	chr3:56727800-56728400	Enhancers	Lung	lung
40	chr3:56727800-56728400	Enhancers	Spleen	Spleen
41	chr3:56727800-56729400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr3:56727800-56731000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:56727800-56731200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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