Variant report

Variant	rs3778652
Chromosome Location	chr6:15455031-15455032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:170078280..170080428-chr6:15454966..15457286,2	MCF-7	breast:
2	chr6:15451813..15454301-chr6:15454611..15456200,2	MCF-7	breast:
3	chr6:15445585..15449236-chr6:15452197..15455366,5	MCF-7	breast:
4	chr6:15446478..15449209-chr6:15454925..15456777,2	K562	blood:
5	chr6:15454081..15456241-chr6:15460942..15462977,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136603	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1474588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076055	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2237117	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2237118	0.84[EUR][1000 genomes]
rs2237121	0.88[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2237124	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2237132	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2237139	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs2237141	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2237145	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2237150	0.81[CEU][hapmap];0.84[GIH][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap]
rs2237153	0.81[CEU][hapmap]
rs2237156	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs2299045	0.89[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2299048	0.96[CEU][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs2299053	0.84[CEU][hapmap]
rs2299054	0.84[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs4085876	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6459406	0.97[EUR][1000 genomes]
rs7754701	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7754755	0.96[EUR][1000 genomes]
rs9349979	0.85[EUR][1000 genomes]
rs9370813	0.84[CEU][hapmap]
rs9370817	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs9370819	0.83[EUR][1000 genomes]
rs9383054	0.84[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs9476827	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][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:119 , 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	chr6:15446000-15456200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:15446000-15459200	Weak transcription	Ovary	ovary
14	chr6:15446000-15462800	Weak transcription	HSMMtube	muscle
15	chr6:15446600-15479800	Weak transcription	Gastric	stomach
16	chr6:15446800-15458600	Weak transcription	Right Ventricle	heart
17	chr6:15447800-15460400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:15448200-15479800	Weak transcription	Pancreas	Pancrea
19	chr6:15449000-15458600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:15449600-15457400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:15449600-15457400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:15449600-15458600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:15449800-15457400	Weak transcription	Brain Angular Gyrus	brain
24	chr6:15449800-15457600	Weak transcription	Placenta	Placenta
25	chr6:15449800-15462800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:15450000-15455200	Weak transcription	Lung	lung
27	chr6:15450000-15456200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:15450000-15457000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:15450000-15458600	Weak transcription	Spleen	Spleen
30	chr6:15450600-15457200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:15451800-15455200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:15452000-15455600	Strong transcription	K562	blood
33	chr6:15452000-15459200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:15452200-15455400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:15452200-15455400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:15452200-15455400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:15452200-15455400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr6:15452200-15455400	Strong transcription	Fetal Muscle Leg	muscle
39	chr6:15452200-15455400	Strong transcription	Thymus	Thymus
40	chr6:15452200-15457200	Weak transcription	Brain Germinal Matrix	brain
41	chr6:15452400-15455200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:15452400-15455400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr6:15452400-15455400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:15452400-15455400	Strong transcription	Fetal Intestine Large	intestine
45	chr6:15452400-15455400	Strong transcription	Fetal Stomach	stomach
46	chr6:15452400-15475800	Weak transcription	Aorta	Aorta
47	chr6:15452600-15455200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:15452600-15455200	Genic enhancers	Brain Substantia Nigra	brain
49	chr6:15452600-15455400	Strong transcription	Primary hematopoietic stem cells	blood
50	chr6:15452600-15455400	Strong transcription	Duodenum Mucosa	Duodenum

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