Variant report

Variant	rs11759978
Chromosome Location	chr6:15462871-15462872
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	chr6:15247011..15249666-chr6:15462121..15464167,2	MCF-7	breast:
3	chr6:15454081..15456241-chr6:15460942..15462977,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235488	Chromatin interaction
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10949302	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11753594	0.92[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11756854	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11756950	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11759250	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16876519	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2327897	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2876393	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41267698	0.81[EUR][1000 genomes]
rs55862621	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55901822	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56070118	0.86[EUR][1000 genomes]
rs56381700	0.81[EUR][1000 genomes]
rs57201697	0.82[AMR][1000 genomes]
rs58121172	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72836316	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72836347	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72837821	0.81[EUR][1000 genomes]
rs72837824	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7768621	0.88[AMR][1000 genomes];0.98[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:120 , 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	chr6:15440000-15468600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:15444600-15477400	Weak transcription	Hela-S3	cervix
4	chr6:15444800-15468800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:15445400-15474000	Weak transcription	NH-A	brain
6	chr6:15446600-15479800	Weak transcription	Gastric	stomach
7	chr6:15448200-15479800	Weak transcription	Pancreas	Pancrea
8	chr6:15452400-15475800	Weak transcription	Aorta	Aorta
9	chr6:15453000-15463000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:15453000-15468600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:15453000-15481000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr6:15453600-15468800	Weak transcription	Dnd41	blood
13	chr6:15454200-15468800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:15454200-15468800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:15455200-15468800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:15455400-15463000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:15455400-15463200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:15455400-15463600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr6:15455400-15468000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:15455400-15468600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:15455400-15468800	Weak transcription	Fetal Intestine Large	intestine
22	chr6:15455400-15468800	Weak transcription	HepG2	liver
23	chr6:15455400-15469600	Weak transcription	Fetal Intestine Small	intestine
24	chr6:15455400-15475600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:15455400-15475600	Weak transcription	Esophagus	oesophagus
26	chr6:15455600-15463000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:15455600-15468600	Weak transcription	K562	blood
28	chr6:15456400-15468600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:15456600-15467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:15457000-15468800	Weak transcription	HMEC	breast
31	chr6:15457000-15480800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:15457400-15463800	Enhancers	Brain Hippocampus Middle	brain
33	chr6:15458400-15484200	Weak transcription	Small Intestine	intestine
34	chr6:15458800-15463800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:15458800-15464000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:15458800-15464400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:15458800-15474600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:15459000-15463200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:15459000-15463600	Weak transcription	Placenta	Placenta
40	chr6:15459200-15464400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:15459200-15464600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:15459200-15468600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:15459400-15468600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:15459400-15468600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:15459600-15463000	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr6:15459800-15463000	Enhancers	Brain Substantia Nigra	brain
47	chr6:15460400-15468600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr6:15460400-15468800	Weak transcription	GM12878-XiMat	blood
49	chr6:15460600-15466400	Weak transcription	Brain Angular Gyrus	brain
50	chr6:15460600-15469000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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