Variant report

Variant	rs9328229
Chromosome Location	chr6:4253413-4253414
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4252767..4255076-chr6:4255779..4258262,2	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10080414	0.88[EUR][1000 genomes]
rs10223886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10428864	0.89[EUR][1000 genomes]
rs1072903	0.88[EUR][1000 genomes]
rs11961149	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11970375	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11970430	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1591412	0.91[EUR][1000 genomes]
rs17500205	0.94[EUR][1000 genomes]
rs17538963	0.83[EUR][1000 genomes]
rs17565229	0.95[EUR][1000 genomes]
rs1832060	0.91[EUR][1000 genomes]
rs2210761	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2210762	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2326473	0.91[EUR][1000 genomes]
rs4255019	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4256473	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4317452	0.83[EUR][1000 genomes]
rs4354197	0.83[EUR][1000 genomes]
rs4443539	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4475361	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4526241	0.91[EUR][1000 genomes]
rs4596533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4629733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4959937	0.88[EUR][1000 genomes]
rs4959938	0.88[EUR][1000 genomes]
rs57509474	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58402712	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59706955	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60023788	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61604146	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6597046	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6597047	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6597048	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6913742	0.89[EUR][1000 genomes]
rs6916181	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6922330	0.90[EUR][1000 genomes]
rs6931784	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6934489	0.90[EUR][1000 genomes]
rs6934652	0.90[EUR][1000 genomes]
rs73356806	0.83[EUR][1000 genomes]
rs73358820	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73358823	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73358854	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73360930	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73360933	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73360945	0.99[EUR][1000 genomes]
rs7754298	0.95[EUR][1000 genomes]
rs7759565	0.88[EUR][1000 genomes]
rs7763657	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7763789	0.98[EUR][1000 genomes]
rs7765457	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs913405	0.94[EUR][1000 genomes]
rs9328227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9328230	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9328231	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9328232	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9328233	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9328236	0.99[EUR][1000 genomes]
rs9392032	0.90[EUR][1000 genomes]
rs9392578	0.86[EUR][1000 genomes]
rs9392580	0.88[EUR][1000 genomes]
rs9405228	0.90[EUR][1000 genomes]
rs9502148	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9502149	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9502150	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9502151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9502152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9502153	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9502154	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9502157	0.99[EUR][1000 genomes]
rs9502158	0.99[EUR][1000 genomes]
rs9502159	0.99[EUR][1000 genomes]
rs9502160	0.98[EUR][1000 genomes]
rs9502161	0.93[EUR][1000 genomes]
rs9502163	0.94[EUR][1000 genomes]
rs9503948	0.83[EUR][1000 genomes]
rs9503953	0.83[EUR][1000 genomes]
rs9503982	0.91[EUR][1000 genomes]
rs9503983	0.91[EUR][1000 genomes]
rs9503984	0.91[EUR][1000 genomes]
rs9503985	0.89[EUR][1000 genomes]
rs9503993	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9503994	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9503995	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9503996	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9504004	0.83[AMR][1000 genomes]
rs9504005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9504006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9504007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9504008	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9504009	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9504010	0.98[EUR][1000 genomes]
rs9504022	0.99[EUR][1000 genomes]
rs9504025	0.94[EUR][1000 genomes]
rs9504033	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	nsv600861	chr6:4238488-4469641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv462618	chr6:4238488-4472587	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv600862	chr6:4238488-4472587	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv949364	chr6:4253413-4466981	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9328229	CDYL	cis	parietal	SCAN
rs9328229	PECI	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4253200-4254000	Enhancers	Adipose Nuclei	Adipose
2	chr6:4253200-4254000	Enhancers	Stomach Smooth Muscle	stomach
3	chr6:4253200-4254200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr6:4253200-4254200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:4253200-4254400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:4253200-4254600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:4253200-4254600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:4253200-4254800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr6:4253200-4254800	Enhancers	Fetal Muscle Leg	muscle
10	chr6:4253200-4254800	Enhancers	Fetal Stomach	stomach
11	chr6:4253200-4254800	Enhancers	Psoas Muscle	Psoas
12	chr6:4253200-4255000	Enhancers	HUVEC	blood vessel
13	chr6:4253400-4253600	Weak transcription	Spleen	Spleen
14	chr6:4253400-4254000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:4253400-4254000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:4253400-4254200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:4253400-4254400	Enhancers	Lung	lung
18	chr6:4253400-4254400	Enhancers	Pancreas	Pancrea
19	chr6:4253400-4254600	Enhancers	Primary hematopoietic stem cells	blood
20	chr6:4253400-4254600	Enhancers	Placenta	Placenta
21	chr6:4253400-4254600	Enhancers	Left Ventricle	heart
22	chr6:4253400-4254600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr6:4253400-4254600	Enhancers	NHDF-Ad	bronchial
24	chr6:4253400-4254800	Enhancers	Colon Smooth Muscle	Colon
25	chr6:4253400-4254800	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr6:4253400-4254800	Enhancers	Fetal Lung	lung
27	chr6:4253400-4254800	Enhancers	Fetal Thymus	thymus
28	chr6:4253400-4254800	Enhancers	Rectal Smooth Muscle	rectum
29	chr6:4253400-4254800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:4253400-4255000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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