Variant report

Variant	rs7177462
Chromosome Location	chr15:83732905-83732906
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:83731135-83732975	K562	blood:	n/a	n/a
2	POLR2A	chr15:83732868-83733068	MCF10A-Er-Src	breast:	n/a	n/a
3	FOXA2	chr15:83732638-83732989	HepG2	liver:	n/a	n/a
4	FOXA1	chr15:83732648-83733103	HepG2	liver:	n/a	n/a
5	CHD1	chr15:83732419-83733082	GM12878	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:83731812..83734557-chr15:83779300..83781603,2	K562	blood:
2	chr15:83731597..83733355-chr15:83864514..83866246,2	K562	blood:
3	chr15:83732514..83734789-chr15:83841378..83843328,2	MCF-7	breast:
4	chr15:83731060..83733792-chr15:83908261..83911046,2	K562	blood:
5	chr15:83716790..83719307-chr15:83732798..83735567,2	MCF-7	breast:
6	chr15:83678535..83684480-chr15:83731660..83738533,12	MCF-7	breast:
7	chr15:83684703..83687598-chr15:83730655..83733296,2	K562	blood:
8	chr15:83731075..83738271-chr15:83771545..83781798,12	K562	blood:
9	chr15:83728223..83733279-chr15:83872338..83876797,5	MCF-7	breast:
10	chr15:83731888..83734386-chr15:83806959..83808488,2	K562	blood:
11	chr15:83730196..83733187-chr15:83768723..83771408,2	K562	blood:
12	chr15:83684589..83686265-chr15:83730370..83733896,3	K562	blood:

No data

Variant related genes	Relation type
MIR4515	TF binding region
ENSG00000249214	Chromatin interaction
ENSG00000169609	Chromatin interaction
ENSG00000166503	Chromatin interaction
ENSG00000136404	Chromatin interaction
ENSG00000260608	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1010820	0.85[GIH][hapmap]
rs11259903	0.82[EUR][1000 genomes]
rs11856000	0.81[EUR][1000 genomes]
rs11857990	0.81[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs11858468	0.85[GIH][hapmap]
rs12440265	0.84[GIH][hapmap]
rs12441585	0.90[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12442572	0.82[EUR][1000 genomes]
rs17158080	0.90[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs17295457	1.00[CHD][hapmap]
rs17361375	0.85[GIH][hapmap]
rs2034617	0.85[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs28373753	0.81[EUR][1000 genomes]
rs28429062	1.00[CHD][hapmap]
rs28436027	0.95[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs28623260	0.82[EUR][1000 genomes]
rs28625676	0.82[EUR][1000 genomes]
rs28662361	1.00[CHD][hapmap]
rs28711332	1.00[CHD][hapmap]
rs28754750	0.83[EUR][1000 genomes]
rs56391827	0.84[EUR][1000 genomes]
rs6603042	0.95[GIH][hapmap];0.81[MEX][hapmap];0.80[EUR][1000 genomes]
rs6603047	0.95[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs716886	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170046	1.00[CHD][hapmap]
rs7180407	0.90[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs8027193	0.90[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs8031723	0.85[GIH][hapmap]
rs8035810	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs8037783	0.90[CEU][hapmap];0.81[EUR][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	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7177462	WHAMM	cis	parietal	SCAN
rs7177462	C15orf40	cis	parietal	SCAN
rs7177462	BTBD1	cis	parietal	SCAN
rs7177462	ARNT2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83700400-83734400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:83725000-83733800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:83725400-83734600	Weak transcription	Placenta	Placenta
4	chr15:83725600-83734400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:83726800-83733600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:83727400-83734200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:83729400-83733200	Enhancers	Fetal Intestine Large	intestine
8	chr15:83729600-83733000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr15:83729600-83733800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:83729600-83733800	Enhancers	Fetal Kidney	kidney
11	chr15:83729800-83733600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr15:83729800-83733600	Enhancers	Fetal Heart	heart
13	chr15:83729800-83733800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr15:83729800-83734400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr15:83730000-83733400	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr15:83730200-83733000	Enhancers	Osteobl	bone
17	chr15:83730200-83733200	Enhancers	NH-A	brain
18	chr15:83730200-83733400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr15:83730200-83733600	Enhancers	NHDF-Ad	bronchial
20	chr15:83730200-83734600	Enhancers	Small Intestine	intestine
21	chr15:83730400-83733200	Enhancers	Fetal Intestine Small	intestine
22	chr15:83730400-83734400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr15:83730400-83734600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:83730600-83733400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:83730600-83733600	Enhancers	Adipose Nuclei	Adipose
26	chr15:83730600-83734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:83730600-83734400	Weak transcription	Esophagus	oesophagus
28	chr15:83730600-83734400	Weak transcription	Lung	lung
29	chr15:83731000-83733200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:83731000-83733600	Weak transcription	HSMMtube	muscle
31	chr15:83731000-83734200	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr15:83731200-83733000	Enhancers	Brain Angular Gyrus	brain
33	chr15:83731200-83733000	Transcr. at gene 5' and 3'	Dnd41	blood
34	chr15:83731200-83733000	Flanking Active TSS	GM12878-XiMat	blood
35	chr15:83731200-83733400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:83731200-83734400	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr15:83731400-83733000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:83731400-83733000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:83731400-83733000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr15:83731400-83733200	Transcr. at gene 5' and 3'	K562	blood
41	chr15:83731400-83733400	Enhancers	Brain Germinal Matrix	brain
42	chr15:83731400-83733800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr15:83731400-83733800	Enhancers	Brain Substantia Nigra	brain
44	chr15:83731400-83734400	Enhancers	Primary B cells from peripheral blood	blood
45	chr15:83731400-83736800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:83731600-83733200	Enhancers	Primary T cells from cord blood	blood
47	chr15:83731600-83733400	Enhancers	Primary hematopoietic stem cells	blood
48	chr15:83731600-83733400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:83731600-83733800	Weak transcription	Colonic Mucosa	Colon
50	chr15:83731600-83734600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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