Variant report

Variant	rs2299043
Chromosome Location	chr6:15457170-15457171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15456622..15459538-chr6:15460887..15465633,6	MCF-7	breast:
2	chr6:15456242..15458163-chr6:15473643..15476148,2	K562	blood:
3	chr6:15456384..15458353-chr6:15458508..15460515,2	K562	blood:
4	chr3:170078280..170080428-chr6:15454966..15457286,2	MCF-7	breast:
5	chr6:15456340..15458507-chr6:15459098..15460711,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136603	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11964846	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs11966626	0.82[EUR][1000 genomes]
rs13192234	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs13192892	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13194650	0.86[EUR][1000 genomes]
rs13196869	0.85[EUR][1000 genomes]
rs13198780	0.85[EUR][1000 genomes]
rs13202100	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13202955	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13204842	0.86[EUR][1000 genomes]
rs13208563	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13209668	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17455404	1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1967664	0.84[EUR][1000 genomes]
rs2076056	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2237138	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35868206	0.87[EUR][1000 genomes]
rs3819396	1.00[CEU][hapmap];0.91[GIH][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs4712251	0.85[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4715975	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4715979	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4715980	1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs6899342	0.86[EUR][1000 genomes]
rs6899343	0.86[EUR][1000 genomes]
rs6917591	1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs742099	1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs742100	0.95[CEU][hapmap];0.95[GIH][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs7756331	0.85[EUR][1000 genomes]
rs7761778	0.85[EUR][1000 genomes]
rs7769291	0.95[CEU][hapmap];0.91[GIH][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs9383056	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9383062	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15435800-15487600	Weak transcription	Colonic Mucosa	Colon
2	chr6:15439000-15458000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:15440000-15468600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:15444600-15477400	Weak transcription	Hela-S3	cervix
5	chr6:15444800-15457200	Weak transcription	Fetal Heart	heart
6	chr6:15444800-15468800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:15445400-15457600	Weak transcription	Fetal Brain Male	brain
8	chr6:15445400-15458600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:15445400-15474000	Weak transcription	NH-A	brain
10	chr6:15445600-15462600	Weak transcription	NHLF	lung
11	chr6:15445800-15460000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:15446000-15459200	Weak transcription	Ovary	ovary
13	chr6:15446000-15462800	Weak transcription	HSMMtube	muscle
14	chr6:15446600-15479800	Weak transcription	Gastric	stomach
15	chr6:15446800-15458600	Weak transcription	Right Ventricle	heart
16	chr6:15447800-15460400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:15448200-15479800	Weak transcription	Pancreas	Pancrea
18	chr6:15449000-15458600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:15449600-15457400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:15449600-15457400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:15449600-15458600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:15449800-15457400	Weak transcription	Brain Angular Gyrus	brain
23	chr6:15449800-15457600	Weak transcription	Placenta	Placenta
24	chr6:15449800-15462800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:15450000-15458600	Weak transcription	Spleen	Spleen
26	chr6:15450600-15457200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:15452000-15459200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr6:15452200-15457200	Weak transcription	Brain Germinal Matrix	brain
29	chr6:15452400-15475800	Weak transcription	Aorta	Aorta
30	chr6:15452600-15457800	Weak transcription	Small Intestine	intestine
31	chr6:15453000-15460800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr6:15453000-15463000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:15453000-15468600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:15453000-15481000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:15453600-15459000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr6:15453600-15459200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr6:15453600-15468800	Weak transcription	Dnd41	blood
38	chr6:15453800-15457600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:15453800-15457600	Weak transcription	Fetal Brain Female	brain
40	chr6:15453800-15459200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:15453800-15462600	Weak transcription	Osteobl	bone
42	chr6:15453800-15462800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr6:15454000-15461600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:15454000-15462600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:15454200-15457200	Weak transcription	Fetal Lung	lung
46	chr6:15454200-15457400	Weak transcription	Brain Hippocampus Middle	brain
47	chr6:15454200-15462600	Weak transcription	HSMM	muscle
48	chr6:15454200-15468800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr6:15454200-15468800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr6:15454400-15458200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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