Variant report

Variant	rs4752973
Chromosome Location	chr11:47269159-47269160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr11:47268991-47271448	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:47269080-47269280	Hela-S3	cervix:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47197588..47201043-chr11:47267472..47270431,4	MCF-7	breast:
2	chr11:47268496..47273681-chr11:47277782..47283365,10	K562	blood:
3	chr11:47234882..47238296-chr11:47268822..47272499,5	MCF-7	breast:
4	chr11:47267134..47271941-chr11:47277592..47282899,11	MCF-7	breast:
5	chr11:47268303..47273264-chr11:47289525..47294481,12	K562	blood:
6	chr11:47263865..47272320-chr11:47288426..47294726,14	MCF-7	breast:
7	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
8	chr11:47201377..47203716-chr11:47267132..47269463,2	K562	blood:
9	chr11:47267881..47272421-chr11:47288787..47294481,12	K562	blood:
10	chr11:47197356..47201056-chr11:47268366..47272336,6	MCF-7	breast:
11	chr11:47263774..47268457-chr11:47268937..47272422,6	MCF-7	breast:
12	chr11:47235800..47238158-chr11:47268993..47270943,3	MCF-7	breast:
13	chr11:47205635..47209843-chr11:47268961..47271979,7	MCF-7	breast:
14	chr11:47268938..47272778-chr11:47288986..47293565,7	MCF-7	breast:

No data

Variant related genes	Relation type
ACP2	TF binding region
NR1H3	TF binding region
ENSG00000134574	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000256746	Chromatin interaction
ENSG00000149182	Chromatin interaction
ENSG00000025434	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1051006	0.87[ASW][hapmap];1.00[MEX][hapmap]
rs1052373	0.82[MEX][hapmap]
rs10769253	1.00[MEX][hapmap]
rs10769255	1.00[MEX][hapmap]
rs10838681	0.86[MEX][hapmap]
rs10838687	0.94[ASW][hapmap];0.84[CEU][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes]
rs10838689	1.00[MEX][hapmap]
rs10838692	0.82[MEX][hapmap]
rs11039144	0.96[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11039148	0.95[AMR][1000 genomes]
rs1449627	0.82[MEX][hapmap]
rs16938581	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs2013867	0.82[CHB][hapmap]
rs2167079	0.82[CHB][hapmap]
rs2242261	0.94[ASW][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2242262	0.86[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2279238	0.94[ASW][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap]
rs2290146	0.87[ASW][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap]
rs2290148	0.87[ASW][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap]
rs2305280	0.94[ASW][hapmap];0.80[CHD][hapmap];0.80[LWK][hapmap];0.86[YRI][hapmap]
rs2306353	0.86[CHB][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2596397	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2596398	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2633080	0.88[AMR][1000 genomes]
rs2633082	0.84[ASN][1000 genomes]
rs2633083	0.97[AMR][1000 genomes]
rs2957873	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs326222	0.82[CHB][hapmap]
rs326224	0.86[AMR][1000 genomes]
rs35879051	0.88[AFR][1000 genomes]
rs3758669	0.87[AFR][1000 genomes]
rs3758670	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs3758673	0.82[ASW][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];0.80[YRI][hapmap]
rs3781619	0.94[ASW][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs3781620	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs3824866	0.86[CHB][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes]
rs4647725	0.86[AMR][1000 genomes]
rs4647726	0.86[AMR][1000 genomes]
rs4647737	0.96[AMR][1000 genomes]
rs4647741	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs4647754	0.96[AMR][1000 genomes]
rs4647757	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4752972	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs4752977	0.87[ASW][hapmap];0.95[MEX][hapmap];0.86[YRI][hapmap]
rs4752979	0.82[EUR][1000 genomes]
rs4752983	0.94[ASW][hapmap];1.00[MEX][hapmap]
rs59663860	0.88[AFR][1000 genomes]
rs6485751	0.83[EUR][1000 genomes]
rs7118396	0.94[ASW][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7120118	0.83[LWK][hapmap];0.82[MEX][hapmap];0.80[YRI][hapmap]
rs7120158	0.86[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7124958	0.81[YRI][hapmap]
rs7395496	0.90[YRI][hapmap];0.87[AMR][1000 genomes]
rs7395581	0.82[ASW][hapmap];0.83[LWK][hapmap];0.83[YRI][hapmap]
rs753992	1.00[MEX][hapmap]
rs753993	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7933246	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs7947269	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs830083	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs830084	0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs830085	0.82[ASW][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.83[YRI][hapmap]
rs901746	0.82[CHB][hapmap]

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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4752973	ACP2	cis	multi-tissue	Pritchard
rs4752973	DDB2	cis	lymphoblastoid	seeQTL
rs4752973	MTCH2	cis	cerebellum	SCAN
rs4752973	ACP2	cis	Thyroid	GTEx
rs4752973	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs4752973	MADD	cis	lymphoblastoid	seeQTL
rs4752973	CYTSB	trans	parietal	SCAN
rs4752973	ACP2	cis	lymphoblastoid	seeQTL
rs4752973	MADD	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47238400-47269400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47242400-47269200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:47243600-47269200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr11:47255400-47269200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:47261600-47269600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:47264200-47269200	Weak transcription	Psoas Muscle	Psoas
7	chr11:47264400-47269200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:47264400-47269200	Weak transcription	HSMM	muscle
9	chr11:47264600-47269800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:47267000-47269200	Weak transcription	Fetal Brain Male	brain
11	chr11:47267000-47269400	Weak transcription	HSMMtube	muscle
12	chr11:47267200-47269200	Enhancers	Liver	Liver
13	chr11:47267400-47269200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:47267400-47269600	Weak transcription	Aorta	Aorta
15	chr11:47267600-47269400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr11:47267600-47269400	Weak transcription	A549	lung
17	chr11:47267800-47269200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr11:47267800-47269200	Weak transcription	Primary T cells from cord blood	blood
19	chr11:47267800-47269200	Weak transcription	Esophagus	oesophagus
20	chr11:47267800-47269200	Weak transcription	Fetal Kidney	kidney
21	chr11:47267800-47269200	Weak transcription	HUVEC	blood vessel
22	chr11:47267800-47269400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr11:47267800-47269400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr11:47267800-47269400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:47267800-47269400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:47267800-47269600	Weak transcription	Primary B cells from cord blood	blood
27	chr11:47267800-47269800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:47268000-47269200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr11:47268000-47269400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:47268400-47269200	Enhancers	Brain Germinal Matrix	brain
31	chr11:47268400-47269200	Genic enhancers	K562	blood
32	chr11:47268400-47269600	Genic enhancers	Placenta	Placenta
33	chr11:47268400-47269600	Enhancers	Right Atrium	heart
34	chr11:47268400-47269600	Genic enhancers	Spleen	Spleen
35	chr11:47268600-47269200	Enhancers	Colonic Mucosa	Colon
36	chr11:47268600-47269200	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr11:47268600-47269400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr11:47268600-47269400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr11:47268600-47269400	Enhancers	Right Ventricle	heart
40	chr11:47268600-47269600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr11:47268600-47269600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:47268600-47269600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr11:47268600-47269600	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr11:47268600-47269600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
45	chr11:47268600-47269800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr11:47268600-47269800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr11:47268600-47269800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:47268600-47270000	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr11:47268600-47270000	Flanking Active TSS	Dnd41	blood
50	chr11:47268800-47269200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links