Variant report

Variant	rs58415346
Chromosome Location	chr5:154138405-154138406
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154133833..154138436-chr5:154316104..154319386,7	K562	blood:
2	chr5:154137877..154139979-chr5:154223259..154226183,2	MCF-7	breast:
3	chr5:154059219..154066449-chr5:154131053..154139153,28	MCF-7	breast:
4	chr5:154079413..154083903-chr5:154131964..154138437,9	MCF-7	breast:
5	chr5:154133224..154141155-chr5:154235246..154242227,24	MCF-7	breast:
6	chr5:154120475..154122431-chr5:154137952..154140710,2	K562	blood:
7	chr5:154133598..154138734-chr5:154235660..154239806,12	K562	blood:

Variant related genes	Relation type
ENSG00000221552	Chromatin interaction
ENSG00000170271	Chromatin interaction
ENSG00000155508	Chromatin interaction
ENSG00000263478	Chromatin interaction
ENSG00000082516	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1035368	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11167705	0.81[ASN][1000 genomes]
rs12188828	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12300	0.84[EUR][1000 genomes]
rs17116411	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17116414	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17116421	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17116442	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17116534	0.85[EUR][1000 genomes]
rs180846	0.80[EUR][1000 genomes]
rs1974776	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1974777	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2042168	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2112223	0.81[EUR][1000 genomes]
rs2161128	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2258437	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2396999	0.90[EUR][1000 genomes]
rs2431184	0.89[ASN][1000 genomes]
rs2544860	0.81[ASN][1000 genomes]
rs2544866	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544874	0.85[EUR][1000 genomes]
rs2544875	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2544876	0.85[EUR][1000 genomes]
rs2544880	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2544884	0.80[EUR][1000 genomes]
rs255529	0.82[ASN][1000 genomes]
rs2560063	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2644743	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2644744	0.81[EUR][1000 genomes]
rs2644746	0.80[EUR][1000 genomes]
rs2688186	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2688187	0.85[EUR][1000 genomes]
rs2688188	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2688189	0.85[EUR][1000 genomes]
rs2688190	0.85[EUR][1000 genomes]
rs2688191	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2688193	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2688198	0.85[EUR][1000 genomes]
rs2688199	0.82[EUR][1000 genomes]
rs2688200	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2688201	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2688206	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2688208	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs348739	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348748	0.80[EUR][1000 genomes]
rs348749	0.81[EUR][1000 genomes]
rs348750	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348751	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348752	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348754	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs39614	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4354100	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs454161	0.89[ASN][1000 genomes]
rs4958771	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55770418	0.80[EUR][1000 genomes]
rs56374414	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59525998	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59749917	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6873483	0.81[ASN][1000 genomes]
rs6879277	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6884416	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs702742	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73276742	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73280705	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7723269	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7728194	0.91[EUR][1000 genomes]
rs816717	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816718	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816720	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs816722	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs816734	0.84[ASN][1000 genomes]
rs816743	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs960499	0.86[ASN][1000 genomes]
rs9942412	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][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	nsv1021153	chr5:154099869-154147970	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	esv3406300	chr5:154133209-154138557	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154134000-154138600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:154134400-154138800	Active TSS	H1 Cell Line	embryonic stem cell
3	chr5:154135800-154139600	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr5:154136800-154138800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:154137200-154138800	Enhancers	Spleen	Spleen
6	chr5:154137200-154139600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:154137200-154139600	Weak transcription	Esophagus	oesophagus
8	chr5:154137200-154139600	Weak transcription	Left Ventricle	heart
9	chr5:154137200-154140000	Weak transcription	Gastric	stomach
10	chr5:154137200-154140800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:154137200-154142400	Enhancers	Primary B cells from peripheral blood	blood
12	chr5:154137400-154139000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr5:154137400-154139400	Enhancers	Stomach Mucosa	stomach
14	chr5:154137400-154141200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr5:154137600-154138600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr5:154137600-154138800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:154137600-154138800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:154137600-154138800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr5:154137600-154138800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:154137600-154138800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr5:154137600-154138800	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr5:154137600-154139000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:154137600-154139000	Flanking Active TSS	HepG2	liver
24	chr5:154137600-154139400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:154137600-154139600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr5:154137600-154139600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr5:154137600-154139600	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr5:154137800-154138800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr5:154137800-154138800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:154137800-154138800	Enhancers	Fetal Muscle Leg	muscle
31	chr5:154137800-154139200	Flanking Active TSS	NHEK	skin
32	chr5:154137800-154139400	Enhancers	Brain Substantia Nigra	brain
33	chr5:154137800-154139600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr5:154137800-154139600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr5:154137800-154140600	Transcr. at gene 5' and 3'	K562	blood
36	chr5:154137800-154141400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr5:154137800-154144000	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr5:154138000-154138800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:154138000-154138800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:154138000-154138800	Enhancers	Fetal Intestine Small	intestine
41	chr5:154138000-154138800	Enhancers	Fetal Thymus	thymus
42	chr5:154138000-154138800	Enhancers	Thymus	Thymus
43	chr5:154138000-154138800	Enhancers	HSMM	muscle
44	chr5:154138000-154139400	Enhancers	Fetal Stomach	stomach
45	chr5:154138000-154139400	Flanking Active TSS	GM12878-XiMat	blood
46	chr5:154138000-154139600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr5:154138000-154139600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:154138000-154139600	Weak transcription	Colonic Mucosa	Colon
49	chr5:154138000-154141000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr5:154138000-154141200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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