Variant report

Variant	rs6933147
Chromosome Location	chr6:4209535-4209536
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1123555	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752585	0.97[EUR][1000 genomes]
rs11753020	1.00[ASN][1000 genomes]
rs11970115	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13197025	0.97[EUR][1000 genomes]
rs13207648	1.00[ASN][1000 genomes]
rs13213431	1.00[ASN][1000 genomes]
rs1327990	1.00[CHD][hapmap]
rs1360811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17137823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1932186	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002920	0.96[EUR][1000 genomes]
rs2002922	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2326472	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34635954	0.98[EUR][1000 genomes]
rs34697725	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34871965	1.00[ASN][1000 genomes]
rs35389479	1.00[ASN][1000 genomes]
rs35801932	0.97[EUR][1000 genomes]
rs35928057	0.96[EUR][1000 genomes]
rs36042165	1.00[ASN][1000 genomes]
rs36099042	1.00[ASN][1000 genomes]
rs6597033	0.97[EUR][1000 genomes]
rs6597034	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6597035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6597038	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6912138	0.98[EUR][1000 genomes]
rs6912707	0.97[EUR][1000 genomes]
rs6932643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938649	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71555837	1.00[ASN][1000 genomes]
rs7743925	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7745239	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7748217	1.00[YRI][hapmap]
rs7749039	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7749050	1.00[CEU][hapmap]
rs7749536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7751774	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs7761775	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770426	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9502132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9502133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9502134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9502136	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503947	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9503950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9503952	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503954	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503955	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503958	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503959	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503979	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503980	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9503981	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6933147	FOXF2	cis	cerebellum	SCAN
rs6933147	TSPYL5	trans	cerebellum	SCAN
rs6933147	CDYL	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4207600-4209800	Enhancers	Adipose Nuclei	Adipose
2	chr6:4207600-4209800	Enhancers	Stomach Smooth Muscle	stomach
3	chr6:4207800-4209600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:4207800-4210600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:4207800-4211200	Enhancers	Primary B cells from peripheral blood	blood
6	chr6:4208400-4209600	Enhancers	Primary hematopoietic stem cells	blood
7	chr6:4208400-4210800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:4208400-4211000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr6:4208600-4210400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:4208600-4211000	Enhancers	Primary T cells from cord blood	blood
11	chr6:4208800-4209600	Enhancers	HMEC	breast
12	chr6:4208800-4209800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:4208800-4211200	Weak transcription	Right Atrium	heart
14	chr6:4208800-4212400	Weak transcription	Psoas Muscle	Psoas
15	chr6:4208800-4212400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:4208800-4212600	Weak transcription	Fetal Heart	heart
17	chr6:4209000-4209600	Enhancers	NHEK	skin
18	chr6:4209000-4210800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr6:4209000-4210800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:4209000-4211000	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr6:4209000-4211200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr6:4209200-4209600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:4209200-4209600	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr6:4209200-4209800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:4209200-4209800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:4209200-4210000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr6:4209200-4210600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:4209400-4209800	Enhancers	HUVEC	blood vessel
29	chr6:4209400-4210000	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr6:4209400-4210200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:4209400-4211000	Enhancers	Spleen	Spleen

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