Variant report

Variant	rs28540420
Chromosome Location	chr5:40687463-40687464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40685575..40687656-chr5:40735781..40737891,2	K562	blood:
2	chr5:40683649..40685431-chr5:40686682..40688286,2	K562	blood:
3	chr5:40677704..40682849-chr5:40683671..40689280,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171522	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10036575	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10038769	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10042750	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10055925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10078575	0.85[ASN][1000 genomes]
rs1345778	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4509070	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4957342	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57806386	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60770691	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6860328	0.80[ASN][1000 genomes]
rs6872282	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6873054	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6897169	0.85[ASN][1000 genomes]
rs7716285	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7726270	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7730368	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs980093	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40679000-40689400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr5:40680200-40689600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
3	chr5:40680800-40690800	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr5:40682400-40691400	Weak transcription	Spleen	Spleen
5	chr5:40682800-40688800	Active TSS	Thymus	Thymus
6	chr5:40682800-40691400	Weak transcription	Lung	lung
7	chr5:40683000-40688600	Weak transcription	NHDF-Ad	bronchial
8	chr5:40683000-40688800	Enhancers	Primary B cells from peripheral blood	blood
9	chr5:40683000-40691600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:40683000-40691600	Weak transcription	Esophagus	oesophagus
11	chr5:40683000-40692000	Weak transcription	Gastric	stomach
12	chr5:40683400-40688000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:40683600-40688800	Enhancers	Fetal Lung	lung
14	chr5:40683800-40690200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:40683800-40691600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:40684000-40687800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:40684000-40687800	Weak transcription	Osteobl	bone
18	chr5:40684000-40688000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:40684000-40688000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:40684000-40690200	Weak transcription	Pancreas	Pancrea
21	chr5:40684000-40700600	Weak transcription	Left Ventricle	heart
22	chr5:40684400-40688800	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
23	chr5:40684600-40687600	Weak transcription	HSMMtube	muscle
24	chr5:40684600-40688000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:40684600-40688000	Weak transcription	NH-A	brain
26	chr5:40684600-40691600	Weak transcription	Fetal Stomach	stomach
27	chr5:40684600-40700400	Weak transcription	Right Ventricle	heart
28	chr5:40685000-40688000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr5:40685200-40688000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:40685200-40688200	Weak transcription	Fetal Kidney	kidney
31	chr5:40685200-40688600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:40685400-40687800	Genic enhancers	Primary hematopoietic stem cells	blood
33	chr5:40685400-40690400	Genic enhancers	Primary monocytes fromperipheralblood	blood
34	chr5:40685400-40691800	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:40685400-40692000	Weak transcription	Aorta	Aorta
36	chr5:40685600-40690800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr5:40685800-40687600	Weak transcription	HMEC	breast
38	chr5:40685800-40688000	Weak transcription	Right Atrium	heart
39	chr5:40685800-40688000	Weak transcription	Hela-S3	cervix
40	chr5:40685800-40691600	Weak transcription	Colonic Mucosa	Colon
41	chr5:40686000-40687600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:40686000-40687800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:40686000-40687800	Weak transcription	A549	lung
44	chr5:40686200-40687800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr5:40686200-40688200	Weak transcription	Fetal Intestine Large	intestine
46	chr5:40686400-40687600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr5:40686400-40688000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr5:40686400-40690200	Weak transcription	Fetal Intestine Small	intestine
49	chr5:40686400-40690600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:40686600-40687800	Weak transcription	NHLF	lung

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