Variant report

Variant	rs9462985
Chromosome Location	chr6:44356292-44356293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:44279512..44282294-chr6:44355146..44356851,3	MCF-7	breast:
2	chr6:44355391..44357263-chr6:44358949..44363275,4	MCF-7	breast:
3	chr6:44220564..44222715-chr6:44354509..44356656,2	MCF-7	breast:
4	chr6:44213880..44217687-chr6:44354177..44357164,5	K562	blood:
5	chr6:44307682..44310665-chr6:44355077..44358723,3	K562	blood:
6	chr6:44231894..44233697-chr6:44355459..44357460,2	K562	blood:
7	chr6:44233082..44237547-chr6:44353791..44357282,5	MCF-7	breast:
8	chr6:44356285..44358292-chr6:44361831..44365473,3	K562	blood:
9	chr6:44231291..44234957-chr6:44353668..44356659,3	K562	blood:
10	chr6:44088681..44090812-chr6:44355955..44357719,2	K562	blood:
11	chr6:44279579..44281700-chr6:44353800..44356317,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000146232	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000124608	Chromatin interaction
ENSG00000249481	Chromatin interaction
ENSG00000265700	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10807300	0.86[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs1293205	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1293208	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1296018	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1952979	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2273667	0.84[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs2297331	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297333	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34264814	0.82[AFR][1000 genomes]
rs34753552	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4143678	0.83[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711781	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475426	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs525043	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs526851	0.85[ASN][1000 genomes]
rs545455	0.94[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs548342	0.94[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs557470	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs559035	0.88[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs564988	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs566078	0.84[JPT][hapmap]
rs67182313	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6918742	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs6923521	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6942323	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs864127	0.80[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes]
rs9395017	0.84[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs9462984	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9462989	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9472273	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv1019145	chr6:44313576-44421440	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9462985	CD2AP	cis	cerebellum	SCAN
rs9462985	GPR115	cis	cerebellum	SCAN
rs9462985	CDC5L	cis	parietal	SCAN
rs9462985	RUNX2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44354400-44356400	Active TSS	Brain Germinal Matrix	brain
2	chr6:44354400-44356600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:44354400-44356600	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr6:44354400-44356600	Active TSS	Fetal Muscle Trunk	muscle
5	chr6:44354400-44356600	Active TSS	Stomach Smooth Muscle	stomach
6	chr6:44354400-44356800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:44354400-44356800	Active TSS	Fetal Brain Female	brain
8	chr6:44354400-44356800	Active TSS	Psoas Muscle	Psoas
9	chr6:44354400-44357000	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:44354400-44357200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:44354400-44357200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr6:44354400-44357400	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr6:44354600-44356400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr6:44354600-44356400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:44354600-44356400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:44354600-44356400	Active TSS	Aorta	Aorta
17	chr6:44354600-44356400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr6:44354600-44356400	Active TSS	Left Ventricle	heart
19	chr6:44354600-44356600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr6:44354600-44356600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:44354600-44356600	Active TSS	Right Ventricle	heart
22	chr6:44354600-44356800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:44354600-44357000	Active TSS	A549	lung
24	chr6:44354600-44357200	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr6:44354600-44357200	Active TSS	Ovary	ovary
26	chr6:44354600-44357200	Active TSS	Right Atrium	heart
27	chr6:44354800-44356400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr6:44354800-44356400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:44354800-44356400	Active TSS	Lung	lung
30	chr6:44354800-44356400	Active TSS	Small Intestine	intestine
31	chr6:44354800-44356600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:44354800-44356600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:44354800-44356800	Active TSS	Fetal Intestine Large	intestine
34	chr6:44354800-44357000	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr6:44355000-44356400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:44355000-44356400	Active TSS	Muscle Satellite Cultured Cells	--
37	chr6:44355000-44356400	Active TSS	Brain Anterior Caudate	brain
38	chr6:44355000-44356400	Active TSS	Brain Hippocampus Middle	brain
39	chr6:44355000-44356400	Active TSS	Fetal Intestine Small	intestine
40	chr6:44355000-44356400	Active TSS	HMEC	breast
41	chr6:44355000-44356600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:44355000-44356600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:44355000-44356600	Active TSS	HSMM	muscle
44	chr6:44355000-44356800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:44355000-44356800	Active TSS	NHDF-Ad	bronchial
46	chr6:44355200-44356400	Bivalent/Poised TSS	HepG2	liver
47	chr6:44355800-44356400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:44356000-44356400	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr6:44356000-44356400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:44356000-44356400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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