Variant report

Variant	rs2297333
Chromosome Location	chr6:44355423-44355424
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120729344..120729897-chr6:44355147..44356131,2	HCT-116	colon:
2	chr6:44279512..44282294-chr6:44355146..44356851,3	MCF-7	breast:
3	chr5:172197837..172198617-chr6:44355209..44356148,2	Hela-S3	cervix:
4	chr10:74397336..74398116-chr6:44355396..44356191,2	Hela-S3	cervix:
5	chr6:44355391..44357263-chr6:44358949..44363275,4	MCF-7	breast:
6	chr6:44220564..44222715-chr6:44354509..44356656,2	MCF-7	breast:
7	chr6:44213880..44217687-chr6:44354177..44357164,5	K562	blood:
8	chr6:44307682..44310665-chr6:44355077..44358723,3	K562	blood:
9	chr19:36485825..36486590-chr6:44355188..44355884,2	Hela-S3	cervix:
10	chr6:44233082..44237547-chr6:44353791..44357282,5	MCF-7	breast:
11	chr5:41870219..41871078-chr6:44355052..44355939,2	Hela-S3	cervix:
12	chr6:44231291..44234957-chr6:44353668..44356659,3	K562	blood:
13	chr6:44355078..44355968-chrX:47696084..47696843,2	Hela-S3	cervix:
14	chr6:44279579..44281700-chr6:44353800..44356317,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000146232	Chromatin interaction
ENSG00000083720	Chromatin interaction
ENSG00000120129	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000249481	Chromatin interaction
ENSG00000205138	Chromatin interaction
ENSG00000124608	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000197779	Chromatin interaction
ENSG00000265700	Chromatin interaction
ENSG00000248668	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10807300	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs11961973	0.84[CHB][hapmap]
rs1293205	0.86[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1293208	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1296018	0.86[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1952979	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2273667	0.84[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs2297331	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34753552	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4143678	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711781	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs475426	0.86[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs525043	0.86[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs526851	0.84[ASN][1000 genomes]
rs545455	0.86[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs548342	0.81[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs557470	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs559035	0.86[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs564988	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs67182313	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6918742	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs6923521	0.86[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6942323	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs864127	0.80[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs9395017	0.84[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs9462984	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9462985	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]
rs9462989	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9472273	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[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
rs2297333	GPR115	cis	cerebellum	SCAN
rs2297333	CD2AP	cis	cerebellum	SCAN
rs2297333	RUNX2	cis	cerebellum	SCAN
rs2297333	CDC5L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44354400-44356000	Active TSS	Colonic Mucosa	Colon
2	chr6:44354400-44356000	Active TSS	Pancreas	Pancrea
3	chr6:44354400-44356200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:44354400-44356200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:44354400-44356200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:44354400-44356400	Active TSS	Brain Germinal Matrix	brain
7	chr6:44354400-44356600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:44354400-44356600	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr6:44354400-44356600	Active TSS	Fetal Muscle Trunk	muscle
10	chr6:44354400-44356600	Active TSS	Stomach Smooth Muscle	stomach
11	chr6:44354400-44356800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr6:44354400-44356800	Active TSS	Fetal Brain Female	brain
13	chr6:44354400-44356800	Active TSS	Psoas Muscle	Psoas
14	chr6:44354400-44357000	Active TSS	H1 Cell Line	embryonic stem cell
15	chr6:44354400-44357200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr6:44354400-44357200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr6:44354400-44357400	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr6:44354600-44356200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:44354600-44356200	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr6:44354600-44356200	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr6:44354600-44356200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:44354600-44356200	Active TSS	Brain Substantia Nigra	brain
23	chr6:44354600-44356200	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr6:44354600-44356200	Active TSS	GM12878-XiMat	blood
25	chr6:44354600-44356400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr6:44354600-44356400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:44354600-44356400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:44354600-44356400	Active TSS	Aorta	Aorta
29	chr6:44354600-44356400	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr6:44354600-44356400	Active TSS	Left Ventricle	heart
31	chr6:44354600-44356600	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr6:44354600-44356600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:44354600-44356600	Active TSS	Right Ventricle	heart
34	chr6:44354600-44356800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:44354600-44357000	Active TSS	A549	lung
36	chr6:44354600-44357200	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr6:44354600-44357200	Active TSS	Ovary	ovary
38	chr6:44354600-44357200	Active TSS	Right Atrium	heart
39	chr6:44354800-44355600	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
40	chr6:44354800-44355800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:44354800-44355800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:44354800-44356000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:44354800-44356000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:44354800-44356000	Active TSS	Colon Smooth Muscle	Colon
45	chr6:44354800-44356000	Active TSS	Esophagus	oesophagus
46	chr6:44354800-44356000	Active TSS	Placenta	Placenta
47	chr6:44354800-44356000	Active TSS	Gastric	stomach
48	chr6:44354800-44356000	Active TSS	Spleen	Spleen
49	chr6:44354800-44356200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:44354800-44356200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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