Variant report

Variant	rs1296018
Chromosome Location	chr6:44411948-44411949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:44405048..44409188-chr6:44409781..44413783,5	K562	blood:
2	chr6:44410364..44415906-chr6:44416897..44422592,7	K562	blood:
3	chr6:44406091..44407637-chr6:44410068..44412209,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10807300	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1293205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1293208	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1952979	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2273667	0.90[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2297331	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2297333	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]
rs2894572	0.88[AMR][1000 genomes]
rs34264814	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34753552	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4143678	0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711781	0.86[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs475426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs525043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs526851	0.97[ASN][1000 genomes]
rs532492	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs545455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs548342	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs557470	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs559035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs564988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs566078	0.84[JPT][hapmap]
rs67182313	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6918742	0.84[CHD][hapmap]
rs6923521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6942323	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs864127	0.93[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9369488	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9395016	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9395017	0.90[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9462984	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9462985	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]
rs9462989	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9472273	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[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	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
2	nsv885858	chr6:44385441-44421240	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv885859	chr6:44385441-44422466	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv517370	chr6:44385441-44422689	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv1850024	chr6:44388505-44422689	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1296018	RUNX2	cis	cerebellum	SCAN
rs1296018	GPR115	cis	cerebellum	SCAN
rs1296018	CD2AP	cis	cerebellum	SCAN
rs1296018	CDC5L	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44376800-44424400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:44388400-44424400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:44390200-44420200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr6:44391800-44412600	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:44396600-44432800	Weak transcription	Fetal Kidney	kidney
6	chr6:44398200-44413400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:44398200-44413400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:44398400-44413600	Weak transcription	Brain Angular Gyrus	brain
9	chr6:44398400-44415400	Weak transcription	Small Intestine	intestine
10	chr6:44398600-44419600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:44400600-44413200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:44401600-44412800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:44402000-44413400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:44402200-44413200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:44402200-44414400	Weak transcription	NH-A	brain
16	chr6:44402400-44413200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:44402600-44412000	Weak transcription	Placenta	Placenta
18	chr6:44403600-44412600	Weak transcription	Hela-S3	cervix
19	chr6:44403800-44412000	Weak transcription	Pancreas	Pancrea
20	chr6:44407400-44412200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:44407400-44414000	Weak transcription	HSMM	muscle
22	chr6:44407600-44413600	Weak transcription	NHEK	skin
23	chr6:44407600-44413800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:44407600-44414000	Weak transcription	HMEC	breast
25	chr6:44407800-44413800	Weak transcription	Osteobl	bone
26	chr6:44407800-44416200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:44407800-44419800	Weak transcription	HSMMtube	muscle
28	chr6:44408000-44413800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:44408200-44412000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:44408600-44412000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr6:44408600-44412000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:44408800-44412000	ZNF genes & repeats	Primary B cells from cord blood	blood
33	chr6:44408800-44412000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
34	chr6:44408800-44412200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:44408800-44412400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr6:44409000-44412000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
37	chr6:44409200-44412600	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:44409200-44412800	Weak transcription	K562	blood
39	chr6:44409200-44413400	Weak transcription	HUVEC	blood vessel
40	chr6:44409200-44416400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr6:44409400-44412200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:44409600-44412000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
43	chr6:44409800-44412000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:44410000-44412000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr6:44410000-44416600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:44410000-44424400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:44410000-44424400	Weak transcription	Colonic Mucosa	Colon
48	chr6:44410000-44424400	Weak transcription	Spleen	Spleen
49	chr6:44410200-44412000	Weak transcription	Ovary	ovary
50	chr6:44410200-44413200	Weak transcription	H1 Cell Line	embryonic stem cell

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