Variant report

Variant	rs745299
Chromosome Location	chr15:41249273-41249274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41216845..41219017-chr15:41248901..41250858,2	K562	blood:
2	chr15:41199759..41201940-chr15:41248954..41250742,2	K562	blood:
3	chr15:41235426..41238056-chr15:41249028..41251261,4	MCF-7	breast:
4	chr15:41229339..41231182-chr15:41247878..41250460,2	MCF-7	breast:
5	chr15:41219573..41224863-chr15:41243808..41249661,11	MCF-7	breast:
6	chr15:41208534..41211234-chr15:41247874..41250474,2	K562	blood:
7	chr15:41231034..41235223-chr15:41248876..41252149,4	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-INO80-1	chr15:41249233-41249579	NONHSAT041903

No data

Variant related genes	Relation type
ENSG00000128917	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10851400	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11070313	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11070314	0.92[ASN][1000 genomes]
rs11557249	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11634736	0.90[EUR][1000 genomes]
rs11853377	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11857572	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12593739	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28473405	0.84[TSI][hapmap]
rs28575174	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4923889	0.80[CHD][hapmap]
rs4924520	0.91[ASN][1000 genomes]
rs60588038	0.92[ASN][1000 genomes]
rs7174555	0.91[ASN][1000 genomes]
rs7175269	0.96[CEU][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs8042127	0.82[ASN][1000 genomes]
rs8042230	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv904106	chr15:41221067-41259523	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	esv1794127	chr15:41245289-41276158	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs745299	GPR176	cis	cerebellum	SCAN
rs745299	C15orf62	cis	parietal	SCAN
rs745299	SPINT1	cis	cerebellum	SCAN
rs745299	RASGRP1	cis	parietal	SCAN
rs745299	GPR176	cis	parietal	SCAN
rs745299	NDUFAF1	cis	Muscle Skeletal	GTEx
rs745299	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs745299	NDUFAF1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41246400-41251000	Enhancers	Pancreas	Pancrea
2	chr15:41246400-41251800	Weak transcription	Primary B cells from cord blood	blood
3	chr15:41246400-41251800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr15:41246400-41268200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:41246600-41249600	Weak transcription	Fetal Brain Female	brain
6	chr15:41246600-41249600	Weak transcription	Stomach Mucosa	stomach
7	chr15:41246600-41249800	Weak transcription	Fetal Brain Male	brain
8	chr15:41246600-41249800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:41246600-41252000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr15:41246600-41252000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:41246600-41252400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:41246600-41252600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:41246600-41253400	Enhancers	Fetal Muscle Leg	muscle
14	chr15:41246600-41258200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:41246600-41270000	Weak transcription	HUVEC	blood vessel
16	chr15:41246800-41249400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:41246800-41249800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:41246800-41249800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:41246800-41250000	Weak transcription	HMEC	breast
20	chr15:41246800-41251000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:41246800-41251200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:41246800-41251800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:41246800-41251800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:41246800-41253000	Weak transcription	A549	lung
25	chr15:41246800-41268000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr15:41246800-41268200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:41247200-41249400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:41247200-41250200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr15:41247200-41250400	Enhancers	HSMM	muscle
30	chr15:41247400-41249400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:41247400-41249400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:41247400-41249400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr15:41247400-41249400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:41247400-41249400	Genic enhancers	Lung	lung
35	chr15:41247400-41250200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:41247400-41253600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr15:41247600-41249800	Enhancers	Adipose Nuclei	Adipose
38	chr15:41247600-41250000	Enhancers	Right Atrium	heart
39	chr15:41247600-41250600	Enhancers	Right Ventricle	heart
40	chr15:41247600-41251400	Enhancers	Psoas Muscle	Psoas
41	chr15:41247800-41249400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr15:41247800-41250400	Enhancers	Fetal Heart	heart
43	chr15:41247800-41250600	Enhancers	Left Ventricle	heart
44	chr15:41248000-41249400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:41248000-41249600	Strong transcription	NHLF	lung
46	chr15:41248000-41250000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr15:41248000-41251800	Weak transcription	Hela-S3	cervix
48	chr15:41248200-41250800	Enhancers	Colon Smooth Muscle	Colon
49	chr15:41248400-41249400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:41248400-41250200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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