Variant report

Variant	rs11764584
Chromosome Location	chr7:99753870-99753871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99753814-99754458	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr7:99752644-99756881	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:99752127-99753952	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr7:99753500-99756680	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:99750175-99756739	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr7:99750655-99753889	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr7:99753296-99756629	GM12878	blood:	n/a	n/a
8	POLR2A	chr7:99752086-99754009	K562	blood:	n/a	n/a
9	RCOR1	chr7:99753500-99753898	K562	blood:	n/a	n/a
10	POLR2A	chr7:99753508-99756689	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr7:99753385-99756681	K562	blood:	n/a	n/a
12	POLR2A	chr7:99753269-99755707	GM12891	blood:	n/a	n/a
13	TEAD4	chr7:99753437-99754016	K562	blood:	n/a	n/a
14	POLR2A	chr7:99753697-99753958	GM12878	blood:	n/a	n/a
15	ELF1	chr7:99753745-99754716	GM12878	blood:	n/a	chr7:99754508-99754521
16	POLR2A	chr7:99749956-99756618	K562	blood:	n/a	n/a
17	POLR2A	chr7:99749910-99757285	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr7:99753771-99756658	GM18505	blood:	n/a	n/a
19	POLR2A	chr7:99750585-99756760	K562	blood:	n/a	n/a
20	POLR2A	chr7:99753663-99754353	H1-hESC	embryonic stem cell:	n/a	n/a
21	STAT5A	chr7:99753801-99754172	GM12878	blood:	n/a	n/a
22	POLR2A	chr7:99753570-99755747	GM12878	blood:	n/a	n/a
23	POLR2A	chr7:99752297-99756669	GM12878	blood:	n/a	n/a
24	ZNF143	chr7:99753560-99753874	K562	blood:	n/a	n/a
25	POLR2A	chr7:99753599-99754643	K562	blood:	n/a	n/a
26	POLR2A	chr7:99753770-99754222	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr7:99753766-99755735	K562	blood:	n/a	n/a
28	JUN	chr7:99753414-99755895	K562	blood:	n/a	chr7:99755520-99755533
29	POLR2A	chr7:99750041-99756801	K562	blood:	n/a	n/a
30	POLR2A	chr7:99752578-99756625	HL-60	blood:	n/a	n/a
31	POLR2A	chr7:99753684-99753924	MCF-7	breast:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99753295..99755968-chr7:99764966..99767548,3	K562	blood:
2	chr7:99719816..99722577-chr7:99753597..99756581,3	K562	blood:
3	chr7:99750795..99756202-chr7:99762627..99766634,7	K562	blood:
4	chr7:99752857..99757651-chr7:99763240..99770051,14	MCF-7	breast:
5	chr7:99677781..99680960-chr7:99753334..99755747,3	K562	blood:
6	chr7:99753605..99756389-chr7:100024404..100026585,2	MCF-7	breast:
7	chr7:99696898..99700086-chr7:99750657..99754674,4	MCF-7	breast:
8	chr7:99690528..99692803-chr7:99751485..99754515,3	MCF-7	breast:
9	chr7:99719091..99721941-chr7:99753666..99756777,4	MCF-7	breast:
10	chr7:99751463..99761050-chr7:99772463..99778676,10	K562	blood:
11	chr7:99708863..99711392-chr7:99752836..99754442,2	K562	blood:
12	chr7:99753430..99757124-chr7:99772344..99777147,8	MCF-7	breast:
13	chr7:99753476..99755824-chr7:99801511..99804012,2	MCF-7	breast:
14	chr7:99702646..99704565-chr7:99753499..99755583,2	K562	blood:
15	chr7:99752659..99755597-chr7:99969374..99971671,2	K562	blood:

No data

Variant related genes	Relation type
C7orf43	TF binding region
ENSG00000207757	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000207547	Chromatin interaction
ENSG00000208036	Chromatin interaction
ENSG00000166526	Chromatin interaction
ENSG00000197093	Chromatin interaction
ENSG00000213420	Chromatin interaction
ENSG00000166997	Chromatin interaction
ENSG00000221838	Chromatin interaction
ENSG00000106290	Chromatin interaction
ENSG00000066923	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000085514	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10231604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11771167	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12705070	0.85[YRI][hapmap]
rs12878	0.88[GIH][hapmap];0.88[MEX][hapmap];0.83[ASN][1000 genomes]
rs1527423	0.89[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap]
rs1918352	0.83[EUR][1000 genomes]
rs1918353	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2272337	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2405440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34130487	0.82[AFR][1000 genomes]
rs35042434	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3736590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736591	0.88[GIH][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs3779047	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4424195	0.85[YRI][hapmap]
rs7785392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7787294	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7787492	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7807641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs999885	0.85[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
7	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
8	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
9	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
10	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
12	nsv888773	chr7:99751594-99772298	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11764584	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs11764584	TAF6	cis	Thyroid	GTEx
rs11764584	AP4M1	cis	cerebellum	SCAN
rs11764584	ZKSCAN1	cis	multi-tissue	Pritchard
rs11764584	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs11764584	AP4M1	cis	Artery Tibial	GTEx
rs11764584	ZSCAN21	cis	parietal	SCAN
rs11764584	AP4M1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99747400-99754600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:99747400-99754600	Weak transcription	Fetal Heart	heart
3	chr7:99747400-99754600	Weak transcription	Right Atrium	heart
4	chr7:99747400-99755200	Weak transcription	Psoas Muscle	Psoas
5	chr7:99747400-99755600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr7:99747800-99754600	Weak transcription	HUVEC	blood vessel
7	chr7:99748000-99755200	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr7:99748200-99754200	Weak transcription	Fetal Brain Male	brain
9	chr7:99749000-99754400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:99749000-99754400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:99749200-99754400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
12	chr7:99749200-99754600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:99749200-99755000	Genic enhancers	Fetal Intestine Large	intestine
14	chr7:99749400-99754200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:99749400-99754200	Strong transcription	Fetal Muscle Leg	muscle
16	chr7:99749400-99754400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr7:99749400-99754400	Genic enhancers	Placenta	Placenta
18	chr7:99749400-99754600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:99749400-99754600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:99749400-99754600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr7:99749400-99754600	Strong transcription	Fetal Stomach	stomach
22	chr7:99749400-99754800	Genic enhancers	Fetal Intestine Small	intestine
23	chr7:99749400-99754800	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr7:99749600-99754600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:99749600-99754600	Strong transcription	Brain Anterior Caudate	brain
26	chr7:99750000-99754800	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr7:99750200-99754200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr7:99750200-99754200	Strong transcription	Spleen	Spleen
29	chr7:99750200-99754600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:99750200-99754600	Strong transcription	Osteobl	bone
31	chr7:99750200-99754800	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr7:99750400-99754200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:99750600-99754000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:99750600-99754200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:99750600-99755200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
36	chr7:99750800-99754000	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr7:99750800-99754000	Strong transcription	Thymus	Thymus
38	chr7:99750800-99754000	Genic enhancers	Monocytes-CD14+_RO01746	blood
39	chr7:99750800-99754400	Genic enhancers	Primary monocytes fromperipheralblood	blood
40	chr7:99750800-99754400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr7:99750800-99754400	Strong transcription	Brain Germinal Matrix	brain
42	chr7:99750800-99754800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr7:99751000-99754000	Strong transcription	Liver	Liver
44	chr7:99751000-99754200	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr7:99751000-99754200	Strong transcription	Pancreas	Pancrea
46	chr7:99751000-99754400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr7:99751000-99754400	Strong transcription	Colon Smooth Muscle	Colon
48	chr7:99751000-99754400	Strong transcription	Fetal Brain Female	brain
49	chr7:99751000-99754400	Strong transcription	Left Ventricle	heart
50	chr7:99751000-99754800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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