Variant report

Variant	rs28561975
Chromosome Location	chr5:112429240-112429241
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112428762..112430474-chr5:112437369..112439619,2	K562	blood:
2	chr5:112428215..112429903-chr5:112440936..112443304,2	MCF-7	breast:
3	chr5:112428968..112430788-chr5:112433593..112437336,4	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10038215	1.00[ASN][1000 genomes]
rs10041206	1.00[ASN][1000 genomes]
rs10060897	1.00[ASN][1000 genomes]
rs10074230	1.00[ASN][1000 genomes]
rs10076739	1.00[ASN][1000 genomes]
rs10078365	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13356288	1.00[ASN][1000 genomes]
rs28513913	1.00[ASN][1000 genomes]
rs28627135	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56783601	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58202991	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62373347	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62374677	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62374680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62374681	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62374706	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594676	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594678	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6865450	0.82[AFR][1000 genomes]
rs6894919	1.00[ASN][1000 genomes]
rs7701630	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708596	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728587	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734300	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326876	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:112391600-112439000	Weak transcription	Gastric	stomach
3	chr5:112399000-112432800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:112399800-112441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:112404400-112436800	Weak transcription	Fetal Brain Male	brain
6	chr5:112411000-112431800	Weak transcription	Spleen	Spleen
7	chr5:112411200-112443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:112412000-112435200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:112412200-112432400	Weak transcription	Fetal Intestine Small	intestine
10	chr5:112417800-112436800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:112418400-112441600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:112418600-112436600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:112418600-112441400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:112419600-112436600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:112420800-112436800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:112421000-112430600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:112421000-112431800	Weak transcription	Pancreas	Pancrea
18	chr5:112421000-112437000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:112421000-112439000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:112421400-112437200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:112424200-112435600	Weak transcription	Small Intestine	intestine
22	chr5:112424400-112448000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:112425400-112429400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:112426000-112430600	Weak transcription	NHDF-Ad	bronchial
25	chr5:112426000-112435200	Weak transcription	Adipose Nuclei	Adipose
26	chr5:112426000-112441600	Weak transcription	Colon Smooth Muscle	Colon
27	chr5:112426200-112437400	Weak transcription	Aorta	Aorta
28	chr5:112426200-112445000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:112426400-112430600	Weak transcription	Osteobl	bone
30	chr5:112426600-112429600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:112426600-112435600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:112426600-112453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr5:112426800-112430600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:112426800-112431000	Weak transcription	HUVEC	blood vessel
35	chr5:112426800-112435400	Weak transcription	Fetal Lung	lung
36	chr5:112426800-112450200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:112426800-112450600	Weak transcription	Primary T cells from cord blood	blood
38	chr5:112426800-112450600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:112426800-112453800	Weak transcription	HSMMtube	muscle
40	chr5:112427000-112430400	Weak transcription	Esophagus	oesophagus
41	chr5:112427000-112430400	Weak transcription	Fetal Muscle Leg	muscle
42	chr5:112427000-112430600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr5:112427000-112431600	Weak transcription	Lung	lung
44	chr5:112427000-112440800	Weak transcription	NH-A	brain
45	chr5:112427000-112453800	Weak transcription	Fetal Kidney	kidney
46	chr5:112427200-112434400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:112427200-112448200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr5:112427400-112431600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:112427600-112431800	Weak transcription	Left Ventricle	heart
50	chr5:112427600-112435600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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