Variant report

Variant	rs2578556
Chromosome Location	chr5:5440963-5440964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:5435223..5438170-chr5:5438538..5441518,2	K562	blood:
2	chr5:5438961..5442301-chr5:5442876..5448006,5	K562	blood:
3	chr5:5437487..5442301-chr5:5443164..5446627,5	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1004263	0.83[EUR][1000 genomes]
rs10063885	0.83[EUR][1000 genomes]
rs12653733	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1541799	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560297	0.88[EUR][1000 genomes]
rs2560298	0.86[EUR][1000 genomes]
rs2560299	0.87[EUR][1000 genomes]
rs2560300	0.86[EUR][1000 genomes]
rs2578500	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2578501	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2578548	0.90[EUR][1000 genomes]
rs2578549	0.87[EUR][1000 genomes]
rs2578550	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2578552	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2578553	0.87[EUR][1000 genomes]
rs2578554	0.87[EUR][1000 genomes]
rs2578557	0.85[EUR][1000 genomes]
rs2578558	0.85[EUR][1000 genomes]
rs2578559	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2578564	0.88[EUR][1000 genomes]
rs2619827	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2619844	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2918253	0.85[EUR][1000 genomes]
rs2918260	0.87[EUR][1000 genomes]
rs2918261	0.88[EUR][1000 genomes]
rs2964131	0.84[EUR][1000 genomes]
rs2964155	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964159	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2964160	0.87[EUR][1000 genomes]
rs3097160	0.90[EUR][1000 genomes]
rs3098377	0.87[EUR][1000 genomes]
rs61063822	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6894118	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	nsv1021802	chr5:5415877-5452886	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv528309	chr5:5434937-5452839	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5425000-5443600	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:5425200-5443200	Weak transcription	Fetal Brain Male	brain
3	chr5:5425200-5443600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:5425200-5443600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:5425200-5443600	Weak transcription	Pancreas	Pancrea
6	chr5:5425200-5443800	Weak transcription	Esophagus	oesophagus
7	chr5:5425400-5441400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:5425400-5443600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:5425400-5443800	Weak transcription	Colonic Mucosa	Colon
10	chr5:5425600-5443400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:5425600-5443400	Weak transcription	Brain Germinal Matrix	brain
12	chr5:5425600-5443600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr5:5425600-5443600	Weak transcription	Thymus	Thymus
14	chr5:5425800-5443200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:5426000-5443200	Weak transcription	Brain Anterior Caudate	brain
16	chr5:5428000-5444800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:5428400-5443600	Weak transcription	Right Ventricle	heart
18	chr5:5429600-5443400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:5430200-5478800	Weak transcription	Stomach Mucosa	stomach
20	chr5:5430400-5443600	Weak transcription	Gastric	stomach
21	chr5:5430400-5443600	Weak transcription	Lung	lung
22	chr5:5430800-5460800	Weak transcription	Fetal Heart	heart
23	chr5:5431800-5442200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:5432000-5441200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr5:5432600-5443200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:5432800-5443400	Weak transcription	HMEC	breast
27	chr5:5432800-5443600	Weak transcription	NHEK	skin
28	chr5:5433200-5443200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:5433200-5456800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr5:5433400-5443600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:5433400-5443600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr5:5433400-5443600	Weak transcription	Spleen	Spleen
33	chr5:5433400-5444400	Weak transcription	HUVEC	blood vessel
34	chr5:5433400-5495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:5433600-5441400	Weak transcription	HSMMtube	muscle
36	chr5:5433600-5443600	Weak transcription	Aorta	Aorta
37	chr5:5433600-5443600	Weak transcription	Brain Substantia Nigra	brain
38	chr5:5433600-5443600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr5:5433600-5447200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:5433600-5455400	Weak transcription	Small Intestine	intestine
41	chr5:5433800-5441400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr5:5433800-5443200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr5:5433800-5443400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr5:5433800-5443600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:5433800-5443600	Weak transcription	Brain Angular Gyrus	brain
46	chr5:5433800-5444800	Weak transcription	Colon Smooth Muscle	Colon
47	chr5:5434000-5441400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr5:5434000-5443600	Weak transcription	Ovary	ovary
49	chr5:5434000-5443600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr5:5434000-5443600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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