Variant report

Variant	rs1552077
Chromosome Location	chr15:30071117-30071118
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:30069062..30071900-chr15:30110638..30114646,3	K562	blood:
2	chr15:30066918..30068960-chr15:30070446..30071982,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104067	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10152681	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10775231	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs11073218	0.90[JPT][hapmap]
rs11853814	0.83[LWK][hapmap];0.81[MKK][hapmap]
rs12438925	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs12440211	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12441554	0.82[ASN][1000 genomes]
rs12916720	0.81[LWK][hapmap];0.81[MKK][hapmap]
rs1383315	0.82[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1480503	0.82[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1585900	0.94[CEU][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1679647	0.82[ASN][1000 genomes]
rs1871678	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2032	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2229518	0.82[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs2337167	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs260531	0.89[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs260532	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs260533	0.89[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs260534	0.89[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs260535	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs260538	0.85[ASN][1000 genomes]
rs28675809	0.86[ASN][1000 genomes]
rs2878893	0.82[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs2878905	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4073316	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4362339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4779670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4780258	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4780259	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4780260	0.82[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.87[MKK][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4780263	0.85[ASN][1000 genomes]
rs6495914	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495927	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495935	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495945	0.94[CEU][hapmap]
rs7168919	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs7170406	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs7171815	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7176476	0.82[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7176594	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180387	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs767514	0.82[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs785445	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8023974	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8027827	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv832944	chr15:29861062-30082057	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1851951	chr15:30043659-30178871	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1552077	C15orf2	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30021400-30097200	Weak transcription	Aorta	Aorta
2	chr15:30052600-30089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:30053000-30072600	Weak transcription	Spleen	Spleen
4	chr15:30058600-30092200	Weak transcription	Esophagus	oesophagus
5	chr15:30058600-30106000	Weak transcription	Gastric	stomach
6	chr15:30059800-30086200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:30060600-30071200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:30060800-30076800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:30062400-30072600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:30062800-30096600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:30063000-30072600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:30063600-30072600	Weak transcription	Lung	lung
13	chr15:30063600-30073400	Weak transcription	Fetal Lung	lung
14	chr15:30063800-30076800	Weak transcription	Fetal Kidney	kidney
15	chr15:30063800-30096000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:30063800-30096800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:30064000-30072600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:30064000-30085600	Weak transcription	Fetal Stomach	stomach
19	chr15:30064000-30085800	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:30064200-30071600	Enhancers	Brain Substantia Nigra	brain
21	chr15:30064200-30073600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:30064400-30083800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:30065200-30103400	Weak transcription	Placenta	Placenta
24	chr15:30065600-30072200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:30065600-30085400	Weak transcription	Fetal Intestine Large	intestine
26	chr15:30065600-30090000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:30065600-30094400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:30065600-30094400	Weak transcription	Fetal Intestine Small	intestine
29	chr15:30065600-30108200	Weak transcription	Pancreas	Pancrea
30	chr15:30066000-30072200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:30066400-30071800	Enhancers	Brain Cingulate Gyrus	brain
32	chr15:30067400-30075400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:30067400-30097400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:30067600-30071600	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr15:30067600-30080600	Weak transcription	NHLF	lung
36	chr15:30067800-30072200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:30067800-30072400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:30067800-30075800	Weak transcription	HUVEC	blood vessel
39	chr15:30067800-30076600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr15:30067800-30076800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:30068000-30071800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:30068000-30072400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:30068200-30072000	Weak transcription	HSMM	muscle
44	chr15:30068200-30072400	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr15:30068600-30071600	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr15:30068600-30076800	Weak transcription	Osteobl	bone
47	chr15:30068800-30071200	Enhancers	Liver	Liver
48	chr15:30068800-30071600	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr15:30068800-30071600	Enhancers	HepG2	liver
50	chr15:30068800-30071800	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links