Variant report

Variant	rs7804288
Chromosome Location	chr7:66765880-66765881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:66765701-66766216	GM12891	blood:	n/a	n/a
2	POLR2A	chr7:66765624-66768309	GM12878	blood:	n/a	n/a
3	POU2F2	chr7:66765574-66766117	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:66765596-66766416	GM12892	blood:	n/a	n/a
5	PAX5	chr7:66765809-66765992	GM12878	blood:	n/a	n/a
6	PBX3	chr7:66765839-66766006	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:66765708-66766286	GM12878	blood:	n/a	n/a
8	HEY1	chr7:66765723-66766135	K562	blood:	n/a	n/a
9	POLR2A	chr7:66765702-66766283	GM12891	blood:	n/a	n/a
10	SP1	chr7:66765733-66766078	GM12878	blood:	n/a	n/a
11	RXRA	chr7:66765822-66766074	GM12878	blood:	n/a	chr7:66766011-66766020
12	POLR2A	chr7:66765737-66766198	GM12891	blood:	n/a	n/a
13	POLR2A	chr7:66765763-66766186	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000201565	TF binding region
STAG3L4	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10081382	1.00[ASN][1000 genomes]
rs10243730	1.00[ASN][1000 genomes]
rs10247355	1.00[ASN][1000 genomes]
rs10264939	1.00[ASN][1000 genomes]
rs11766952	1.00[ASN][1000 genomes]
rs11769345	1.00[ASN][1000 genomes]
rs11769406	1.00[ASN][1000 genomes]
rs11770922	1.00[ASN][1000 genomes]
rs11773861	1.00[ASN][1000 genomes]
rs12698570	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13222551	1.00[ASN][1000 genomes]
rs13222852	1.00[ASN][1000 genomes]
rs13222880	1.00[ASN][1000 genomes]
rs13225831	1.00[ASN][1000 genomes]
rs13239441	1.00[ASN][1000 genomes]
rs13241749	1.00[ASN][1000 genomes]
rs13246453	1.00[ASN][1000 genomes]
rs2421427	1.00[ASN][1000 genomes]
rs28524910	1.00[ASN][1000 genomes]
rs28828435	1.00[ASN][1000 genomes]
rs35955950	1.00[ASN][1000 genomes]
rs3980761	1.00[ASN][1000 genomes]
rs4266531	1.00[ASN][1000 genomes]
rs55647045	1.00[ASN][1000 genomes]
rs56081654	1.00[ASN][1000 genomes]
rs56224758	1.00[ASN][1000 genomes]
rs56376467	1.00[ASN][1000 genomes]
rs66521840	1.00[ASN][1000 genomes]
rs66669140	1.00[ASN][1000 genomes]
rs66697341	1.00[ASN][1000 genomes]
rs66701377	1.00[ASN][1000 genomes]
rs67794814	1.00[ASN][1000 genomes]
rs68034409	1.00[ASN][1000 genomes]
rs6958056	1.00[ASN][1000 genomes]
rs6968898	1.00[ASN][1000 genomes]
rs6973163	1.00[ASN][1000 genomes]
rs73144570	1.00[ASN][1000 genomes]
rs7783776	1.00[ASN][1000 genomes]
rs7791848	1.00[ASN][1000 genomes]
rs7791853	0.81[ASW][hapmap];0.84[YRI][hapmap]
rs7792207	1.00[ASN][1000 genomes]
rs7795025	1.00[ASN][1000 genomes]
rs9691420	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1032237	chr7:66644492-66785029	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers 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
5	nsv1027702	chr7:66722103-66841913	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	32 gene(s)	inside rSNPs	diseases
6	nsv1031048	chr7:66722103-66844039	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	nsv8129	chr7:66735416-66766669	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv13926	chr7:66735980-66767830	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv970872	chr7:66742783-66776118	Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7804288	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs7804288	STAG3L4	cis	Nerve Tibial	GTEx
rs7804288	TYW1	cis	Muscle Skeletal	GTEx
rs7804288	TYW1	cis	Esophagus Mucosa	GTEx
rs7804288	TYW1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66694800-66766600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr7:66701600-66766600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr7:66717400-66766200	Weak transcription	Fetal Muscle Leg	muscle
4	chr7:66717400-66766400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr7:66717800-66766400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:66719000-66766400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr7:66719800-66766200	Weak transcription	Spleen	Spleen
8	chr7:66723800-66766400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:66725800-66766200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr7:66725800-66766400	Weak transcription	Adipose Nuclei	Adipose
11	chr7:66727600-66766200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr7:66728600-66766600	Weak transcription	Brain Angular Gyrus	brain
13	chr7:66729000-66767000	Weak transcription	Gastric	stomach
14	chr7:66733200-66766600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:66733400-66766800	Weak transcription	Lung	lung
16	chr7:66736400-66766600	Weak transcription	Brain Substantia Nigra	brain
17	chr7:66742200-66766400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr7:66742400-66766400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:66742600-66766800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:66747600-66766600	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:66748200-66766800	Weak transcription	Ovary	ovary
22	chr7:66748400-66766400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr7:66749600-66766400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:66749600-66766400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:66749600-66766600	Weak transcription	Brain Anterior Caudate	brain
26	chr7:66749600-66766600	Weak transcription	Fetal Intestine Large	intestine
27	chr7:66751000-66766600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr7:66751000-66767000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr7:66751200-66766400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr7:66751800-66766200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr7:66753600-66766200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:66754000-66766600	Weak transcription	Left Ventricle	heart
33	chr7:66754600-66766600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr7:66754800-66766400	Weak transcription	Thymus	Thymus
35	chr7:66755400-66766400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr7:66755800-66766200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:66756000-66766400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:66756000-66766400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr7:66756600-66766600	Weak transcription	Fetal Intestine Small	intestine
40	chr7:66756600-66766600	Weak transcription	Fetal Stomach	stomach
41	chr7:66757000-66766200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr7:66757400-66766200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:66757400-66766600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr7:66763600-66766600	Weak transcription	Primary B cells from cord blood	blood
45	chr7:66765400-66766400	Enhancers	Dnd41	blood
46	chr7:66765400-66766600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr7:66765600-66766800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr7:66765800-66767000	Enhancers	Small Intestine	intestine
49	chr7:66765800-66769000	Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links