Variant report

Variant	rs2469535
Chromosome Location	chr15:76639522-76639523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76628671..76632944-chr15:76633969..76642252,10	MCF-7	breast:
2	chr15:76625840..76631025-chr15:76637216..76641688,7	MCF-7	breast:
3	chr15:76637265..76640642-chr15:76644223..76647135,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159556	Chromatin interaction
ENSG00000140386	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs157762	0.86[AMR][1000 genomes]
rs157775	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs157778	0.81[ASN][1000 genomes]
rs166933	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16968196	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs172244	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1875883	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2078437	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460161	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2469224	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2469554	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2469556	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283796	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs283799	0.85[ASN][1000 genomes]
rs284884	0.86[AMR][1000 genomes]
rs284885	0.92[ASN][1000 genomes]
rs284893	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284897	0.92[ASN][1000 genomes]
rs284898	0.92[ASN][1000 genomes]
rs284901	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs284902	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs284903	0.92[ASN][1000 genomes]
rs284904	0.92[ASN][1000 genomes]
rs284905	0.92[ASN][1000 genomes]
rs284907	0.92[ASN][1000 genomes]
rs2938695	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2944377	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2948703	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2956873	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2957560	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2957607	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2957611	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2957612	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2957613	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs387321	0.92[ASN][1000 genomes]
rs454381	0.86[ASN][1000 genomes]
rs4886491	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886492	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs494268	0.86[AMR][1000 genomes]
rs8031378	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031672	0.87[EUR][1000 genomes];0.96[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	nsv904399	chr15:76622903-76646575	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv525769	chr15:76632487-76661925	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2469535	ISL2	cis	Whole Blood	GTEx
rs2469535	RP11-685G9.2	cis	Whole Blood	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76630200-76641800	Weak transcription	A549	lung
2	chr15:76636400-76640200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:76637200-76640000	Weak transcription	K562	blood
4	chr15:76637800-76640200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:76638000-76639600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
6	chr15:76638000-76639600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
7	chr15:76638000-76639600	Flanking Bivalent TSS/Enh	NHEK	skin
8	chr15:76638000-76639800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:76638000-76639800	Enhancers	Spleen	Spleen
10	chr15:76638000-76640000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr15:76638000-76640000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr15:76638000-76640000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:76638000-76640400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr15:76638200-76639600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
15	chr15:76638200-76639600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
16	chr15:76638200-76639600	Flanking Bivalent TSS/Enh	Placenta	Placenta
17	chr15:76638200-76639600	Active TSS	Hela-S3	cervix
18	chr15:76638200-76639800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr15:76638200-76639800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:76638200-76639800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:76638200-76640000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:76638200-76640000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr15:76638200-76640000	Bivalent Enhancer	Fetal Heart	heart
24	chr15:76638200-76640000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
25	chr15:76638200-76640200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr15:76638200-76640200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:76638400-76639600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:76638400-76639600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:76638400-76639600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
30	chr15:76638400-76639600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
31	chr15:76638400-76639600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
32	chr15:76638400-76639600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
33	chr15:76638400-76639600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:76638400-76639600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:76638400-76639600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
36	chr15:76638400-76639600	Bivalent Enhancer	Fetal Thymus	thymus
37	chr15:76638400-76639600	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
38	chr15:76638400-76639800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
39	chr15:76638400-76639800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
40	chr15:76638400-76640000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:76638400-76640000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
42	chr15:76638600-76639600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr15:76638600-76639600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:76638600-76639600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
45	chr15:76638600-76639600	Active TSS	Gastric	stomach
46	chr15:76638600-76639800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:76638600-76639800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:76638600-76639800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
49	chr15:76638600-76639800	Bivalent/Poised TSS	Esophagus	oesophagus
50	chr15:76638600-76639800	Flanking Bivalent TSS/Enh	Placenta Amnion	Placenta Amnion

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