Variant report

Variant	rs28405838
Chromosome Location	chr15:77226053-77226054
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77196182..77198169-chr15:77222869..77226186,3	K562	blood:
2	chr15:77224127..77226874-chr15:77232246..77234714,2	K562	blood:
3	chr12:120729471..120731046-chr15:77223645..77226365,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000117906	Chromatin interaction
ENSG00000140386	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10431768	0.85[ASN][1000 genomes]
rs12593107	0.86[ASN][1000 genomes]
rs1611866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1813479	0.91[ASN][1000 genomes]
rs1913001	0.90[ASN][1000 genomes]
rs2063542	0.84[ASN][1000 genomes]
rs28421596	0.86[AFR][1000 genomes]
rs28551558	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28618274	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28644501	0.86[AFR][1000 genomes]
rs28744566	0.83[AFR][1000 genomes]
rs3110378	0.81[ASN][1000 genomes]
rs35373913	0.81[ASN][1000 genomes]
rs35645941	0.81[ASN][1000 genomes]
rs3764244	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243043	0.90[ASN][1000 genomes]
rs4541044	0.91[ASN][1000 genomes]
rs4583202	0.85[ASN][1000 genomes]
rs6495222	0.90[ASN][1000 genomes]
rs7172639	0.85[ASN][1000 genomes]
rs7174048	0.80[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	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77224800-77227800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:77224800-77228800	Weak transcription	Gastric	stomach
3	chr15:77224800-77231000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:77224800-77243000	Weak transcription	Lung	lung
5	chr15:77224800-77256000	Weak transcription	Pancreas	Pancrea
6	chr15:77225000-77226200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:77225000-77226200	Enhancers	Small Intestine	intestine
8	chr15:77225000-77226400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:77225000-77226600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:77225000-77226800	Enhancers	Brain Substantia Nigra	brain
11	chr15:77225000-77227200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:77225000-77227800	Weak transcription	Ovary	ovary
13	chr15:77225000-77227800	Weak transcription	Psoas Muscle	Psoas
14	chr15:77225000-77227800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:77225000-77227800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:77225000-77227800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr15:77225000-77228000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:77225000-77228000	Weak transcription	Left Ventricle	heart
19	chr15:77225000-77228400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr15:77225000-77228800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:77225000-77240400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:77225000-77240400	Weak transcription	Spleen	Spleen
23	chr15:77225000-77241000	Weak transcription	Colonic Mucosa	Colon
24	chr15:77225000-77242800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:77225000-77243000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr15:77225000-77245200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:77225000-77245200	Weak transcription	Esophagus	oesophagus
28	chr15:77225000-77247000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:77225000-77254600	Weak transcription	Aorta	Aorta
30	chr15:77225000-77260200	Weak transcription	Right Ventricle	heart
31	chr15:77225200-77226200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr15:77225200-77226200	Weak transcription	Adipose Nuclei	Adipose
33	chr15:77225200-77226200	Enhancers	Fetal Brain Male	brain
34	chr15:77225200-77226400	Enhancers	Brain Hippocampus Middle	brain
35	chr15:77225200-77226400	Genic enhancers	Fetal Lung	lung
36	chr15:77225200-77226800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr15:77225200-77227600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:77225200-77227600	Weak transcription	Fetal Kidney	kidney
39	chr15:77225200-77227600	Weak transcription	HSMMtube	muscle
40	chr15:77225200-77227800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr15:77225200-77245200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:77225200-77246400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr15:77225400-77226200	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr15:77225400-77226200	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr15:77225400-77226200	Enhancers	Fetal Intestine Small	intestine
46	chr15:77225400-77226400	Genic enhancers	HepG2	liver
47	chr15:77225400-77227000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:77225400-77227200	Weak transcription	GM12878-XiMat	blood
49	chr15:77225400-77227600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr15:77225400-77227600	Weak transcription	Rectal Smooth Muscle	rectum

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