Variant report

Variant	rs2465265
Chromosome Location	chr7:27071476-27071477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27071114..27072708-chr7:27126763..27129361,2	K562	blood:
2	7:27071265-27080138..7:27181770-27195105	K562	blood:

Variant related genes	Relation type
ENSG00000254369	Chromatin interaction
ENSG00000106004	Chromatin interaction
ENSG00000106006	Chromatin interaction
ENSG00000272801	Chromatin interaction
ENSG00000105997	Chromatin interaction
ENSG00000273433	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1005977	0.90[EUR][1000 genomes]
rs10231265	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10267442	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1082313	0.86[EUR][1000 genomes]
rs11975480	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11977871	0.90[AFR][1000 genomes]
rs12700771	0.81[AFR][1000 genomes]
rs13311400	0.84[EUR][1000 genomes]
rs2015424	0.92[EUR][1000 genomes]
rs213520	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2252947	0.89[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs2264680	0.93[EUR][1000 genomes]
rs2428420	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2428424	0.91[EUR][1000 genomes]
rs2428426	0.89[EUR][1000 genomes]
rs2428427	0.87[EUR][1000 genomes]
rs2428428	0.90[EUR][1000 genomes]
rs2428430	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2462901	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2462903	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2462905	0.89[EUR][1000 genomes]
rs2462907	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs2465263	0.93[CEU][hapmap]
rs2465267	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2522822	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2522823	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2522829	0.89[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2693658	0.92[EUR][1000 genomes]
rs2693666	0.92[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712231	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712232	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712235	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2712240	0.91[EUR][1000 genomes]
rs2712241	0.93[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712243	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712249	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2936426	0.84[EUR][1000 genomes]
rs2960784	0.84[EUR][1000 genomes]
rs2960786	0.84[EUR][1000 genomes]
rs774248	0.85[EUR][1000 genomes]
rs774254	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs774255	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs774264	0.85[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs774269	0.82[EUR][1000 genomes]
rs799237	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs954051	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1018709	chr7:26990384-27216552	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	nsv538806	chr7:26990384-27216552	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv967485	chr7:27066773-27082518	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2465265	HOXA-AS2	cis	Whole Blood	GTEx
rs2465265	HOTAIRM1	cis	Whole Blood	GTEx
rs2465265	HOXA2	cis	Whole Blood	GTEx
rs2465265	SKAP2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27068200-27071600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:27068400-27071800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
3	chr7:27068600-27071600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr7:27068800-27071800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr7:27069800-27071600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr7:27069800-27071600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr7:27069800-27071800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr7:27070200-27071800	Enhancers	Fetal Thymus	thymus
9	chr7:27070200-27072000	Enhancers	Hela-S3	cervix
10	chr7:27070200-27072200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr7:27070200-27072800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr7:27070200-27072800	Enhancers	NHEK	skin
13	chr7:27070200-27073000	Enhancers	HSMMtube	muscle
14	chr7:27070400-27072800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr7:27070600-27071600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr7:27070600-27072000	Enhancers	Stomach Mucosa	stomach
17	chr7:27070800-27071800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr7:27070800-27072600	Weak transcription	Fetal Muscle Leg	muscle
19	chr7:27071000-27071600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr7:27071000-27071800	Enhancers	Primary B cells from peripheral blood	blood
21	chr7:27071000-27072000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:27071000-27072000	Enhancers	Rectal Smooth Muscle	rectum
23	chr7:27071000-27072200	Enhancers	Primary T cells from cord blood	blood
24	chr7:27071000-27072200	Enhancers	Dnd41	blood
25	chr7:27071000-27072200	Enhancers	HUVEC	blood vessel
26	chr7:27071000-27072600	Enhancers	Fetal Heart	heart
27	chr7:27071000-27072800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr7:27071000-27072800	Enhancers	Fetal Kidney	kidney
29	chr7:27071000-27073200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:27071200-27071600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr7:27071200-27071600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr7:27071200-27071600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr7:27071200-27071600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr7:27071200-27071600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:27071200-27071600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr7:27071200-27071600	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr7:27071200-27071600	Active TSS	NHLF	lung
38	chr7:27071200-27071600	Flanking Active TSS	Osteobl	bone
39	chr7:27071200-27071800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:27071200-27071800	Active TSS	Primary B cells from cord blood	blood
41	chr7:27071200-27071800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr7:27071200-27071800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:27071200-27071800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:27071200-27071800	Enhancers	Adipose Nuclei	Adipose
45	chr7:27071200-27071800	Enhancers	Duodenum Mucosa	Duodenum
46	chr7:27071200-27071800	Bivalent Enhancer	Fetal Lung	lung
47	chr7:27071200-27071800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr7:27071200-27072000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:27071200-27072000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr7:27071200-27072000	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links