Variant report

Variant	rs9468538
Chromosome Location	chr6:11174250-11174251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11173246..11175839-chr6:11231318..11234093,2	MCF-7	breast:
2	chr1:40503937..40506110-chr6:11172221..11174586,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131236	Chromatin interaction
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs3734406	1.00[AMR][1000 genomes]
rs56128589	1.00[AMR][1000 genomes]
rs58174898	1.00[AMR][1000 genomes]
rs73721655	1.00[AMR][1000 genomes]
rs73721660	1.00[AMR][1000 genomes]
rs73721685	1.00[AMR][1000 genomes]
rs73723906	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73723908	1.00[AMR][1000 genomes]
rs73723919	1.00[AMR][1000 genomes]
rs9468564	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9468689	1.00[AMR][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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11162400-11185400	Weak transcription	Esophagus	oesophagus
2	chr6:11169800-11174600	Weak transcription	Left Ventricle	heart
3	chr6:11171800-11185400	Weak transcription	Gastric	stomach
4	chr6:11172800-11175000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:11172800-11195000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:11173200-11174400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr6:11173200-11175800	Weak transcription	Stomach Mucosa	stomach
8	chr6:11173200-11179400	Weak transcription	Placenta	Placenta
9	chr6:11173200-11181600	Weak transcription	Primary T cells from cord blood	blood
10	chr6:11173200-11181600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:11173200-11182400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr6:11173200-11182600	Weak transcription	Primary B cells from cord blood	blood
13	chr6:11173200-11183400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:11173200-11183600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:11173200-11183600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:11173200-11184000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr6:11173200-11184000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:11173200-11184000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:11173200-11184000	Weak transcription	Lung	lung
20	chr6:11173200-11184000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:11173200-11184000	Weak transcription	Spleen	Spleen
22	chr6:11173200-11184200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:11173200-11184600	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:11173200-11184800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:11173200-11184800	Weak transcription	Pancreas	Pancrea
26	chr6:11173200-11185400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:11173200-11185400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:11173200-11185400	Weak transcription	Ovary	ovary
29	chr6:11173200-11187600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:11173400-11178800	Weak transcription	Brain Substantia Nigra	brain
31	chr6:11173400-11180600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr6:11173400-11182200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:11173400-11183200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:11173400-11183600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr6:11173400-11183600	Weak transcription	Osteobl	bone
36	chr6:11173400-11183800	Weak transcription	GM12878-XiMat	blood
37	chr6:11173400-11184000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr6:11173400-11184000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:11173400-11184000	Weak transcription	Aorta	Aorta
40	chr6:11173400-11184200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:11173400-11185400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:11173400-11185400	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:11173400-11185600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:11173600-11179200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:11173600-11181800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:11173600-11184000	Weak transcription	Fetal Kidney	kidney
47	chr6:11173800-11179200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:11173800-11179400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:11173800-11183600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:11173800-11184000	Weak transcription	Thymus	Thymus

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