Variant report

Variant	rs1127648
Chromosome Location	chr15:75967095-75967096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75966856-75967415	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr15:75967018-75967273	HCT-116	colon:	n/a	n/a
3	POLR2A	chr15:75967090-75967295	U87	brain:	n/a	n/a
4	POLR2A	chr15:75966932-75967469	HCT-116	colon:	n/a	n/a
5	POLR2A	chr15:75966549-75967760	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:75961392-75968208	U87	brain:	n/a	n/a
7	POLR2A	chr15:75963030-75967116	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:75959477..75961684-chr15:75965277..75967362,2	K562	blood:
2	chr15:75742474..75744399-chr15:75965512..75967791,2	K562	blood:
3	chr15:75742002..75744391-chr15:75965188..75968465,3	K562	blood:
4	chr15:75965361..75969270-chr15:75970035..75973000,4	K562	blood:
5	chr15:75927186..75935349-chr15:75957229..75967736,17	MCF-7	breast:
6	chr15:75965792..75967454-chr15:75970314..75971867,2	MCF-7	breast:
7	chr15:75951981..75955869-chr15:75961912..75967583,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000203392	TF binding region
ENSG00000260892	TF binding region
ENSG00000177971	Chromatin interaction
ENSG00000260206	Chromatin interaction
ENSG00000203392	Chromatin interaction
ENSG00000169375	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1127646	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11631648	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11634290	0.89[GIH][hapmap];0.80[TSI][hapmap]
rs11634497	0.81[EUR][1000 genomes]
rs11636221	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11636280	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs11636352	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12898809	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900539	0.83[EUR][1000 genomes]
rs4414463	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4592617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886732	0.83[ASN][1000 genomes]
rs7182902	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8027239	0.81[EUR][1000 genomes]
rs8030131	0.88[EUR][1000 genomes]
rs8034760	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
4	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
6	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
7	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
9	nsv904391	chr15:75930757-76001654	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
10	nsv904392	chr15:75930757-76039262	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
11	nsv904393	chr15:75932177-76001654	Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
12	nsv904394	chr15:75948671-76039262	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv904395	chr15:75957928-75984095	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
14	nsv904396	chr15:75961518-76071105	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
15	nsv569997	chr15:75965169-75991451	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1127648	CSPG4	cis	parietal	SCAN
rs1127648	MYO9A	cis	parietal	SCAN
rs1127648	ETFA	cis	parietal	SCAN
rs1127648	PTPN9	cis	cerebellum	SCAN
rs1127648	SCAMP5	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75953000-75969600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:75957800-75967200	Enhancers	Placenta Amnion	Placenta Amnion
3	chr15:75958200-75967200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:75959400-75967600	Weak transcription	Liver	Liver
5	chr15:75961000-75968200	Enhancers	NHDF-Ad	bronchial
6	chr15:75962400-75968600	Enhancers	Adipose Nuclei	Adipose
7	chr15:75962400-75968800	Enhancers	Right Ventricle	heart
8	chr15:75962400-75969000	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr15:75963200-75968400	Enhancers	Placenta	Placenta
10	chr15:75963400-75968000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:75963800-75968200	Enhancers	Left Ventricle	heart
12	chr15:75964000-75967400	Enhancers	Fetal Heart	heart
13	chr15:75964200-75968600	Enhancers	Ovary	ovary
14	chr15:75964200-75969200	Enhancers	Right Atrium	heart
15	chr15:75964800-75967200	Enhancers	Brain Substantia Nigra	brain
16	chr15:75964800-75968400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:75965000-75967600	Enhancers	Brain Hippocampus Middle	brain
18	chr15:75965000-75968000	Enhancers	Brain Anterior Caudate	brain
19	chr15:75965200-75968400	Enhancers	Psoas Muscle	Psoas
20	chr15:75965600-75968800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:75965600-75978400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:75965800-75967200	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr15:75965800-75967200	Enhancers	Rectal Smooth Muscle	rectum
24	chr15:75965800-75967400	Enhancers	NH-A	brain
25	chr15:75965800-75967600	Weak transcription	Spleen	Spleen
26	chr15:75965800-75969800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:75965800-75986000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:75966000-75967400	Enhancers	Colon Smooth Muscle	Colon
29	chr15:75966000-75968000	Weak transcription	Lung	lung
30	chr15:75966000-75968200	Weak transcription	Gastric	stomach
31	chr15:75966000-75968400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:75966000-75972400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr15:75966200-75967600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:75966200-75967600	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr15:75966200-75967800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:75966200-75968000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr15:75966200-75969600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:75966200-75971000	Weak transcription	NHEK	skin
39	chr15:75966200-75971200	Genic enhancers	Fetal Intestine Small	intestine
40	chr15:75966200-75974400	Weak transcription	Pancreas	Pancrea
41	chr15:75966400-75967400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:75966400-75968000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:75966400-75968600	Weak transcription	Aorta	Aorta
44	chr15:75966400-75969600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:75966400-75972600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:75966400-75972800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:75966400-75979000	Weak transcription	HMEC	breast
48	chr15:75966400-75993200	Weak transcription	Hela-S3	cervix
49	chr15:75966600-75967200	Enhancers	Stomach Smooth Muscle	stomach
50	chr15:75966600-75968200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links