Variant report

Variant	rs10810579
Chromosome Location	chr9:16625061-16625062
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	GATA3	chr9:16624767-16627415	SK-N-SH	brain:	n/a	chr9:16625491-16625501 chr9:16626394-16626404
2	EP300	chr9:16624848-16625448	SK-N-SH_RA	brain:	n/a	n/a
3	POLR2A	chr9:16624776-16625448	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr9:16624777-16627480	SK-N-SH	brain:	n/a	chr9:16626072-16626082
5	RAD21	chr9:16624813-16625095	SK-N-SH_RA	brain:	n/a	n/a
6	EP300	chr9:16624848-16625491	SK-N-SH_RA	brain:	n/a	n/a
7	PBX3	chr9:16624816-16625544	SK-N-SH	brain:	n/a	n/a
8	EP300	chr9:16624895-16627450	SK-N-SH	brain:	n/a	chr9:16625489-16625503 chr9:16626011-16626019 chr9:16625521-16625534 chr9:16626808-16626817 chr9:16626807-16626816 chr9:16626010-16626024
9	POLR2A	chr9:16624912-16625082	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ENSG00000230694	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1003069	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1003070	0.81[EUR][1000 genomes]
rs1029015	0.85[CHB][hapmap]
rs10756773	0.90[CHB][hapmap]
rs10810580	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs10810581	0.89[CEU][hapmap];0.84[YRI][hapmap];0.80[EUR][1000 genomes]
rs10962519	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs10962520	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs11790341	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.84[ASN][1000 genomes]
rs13290470	0.92[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1415471	0.84[CHB][hapmap]
rs1890074	0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2050617	1.00[CHB][hapmap]
rs2275256	0.84[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4961722	0.81[CEU][hapmap]
rs4961727	0.80[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs4961728	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7019299	1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs7033512	1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7043298	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[ASN][1000 genomes]
rs7046245	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv430000	chr9:16603483-16671045	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16611400-16626400	Weak transcription	Aorta	Aorta
2	chr9:16613800-16625600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:16614400-16625400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:16615600-16625400	Weak transcription	Psoas Muscle	Psoas
5	chr9:16618600-16625400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:16618800-16625400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:16620200-16625200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:16621400-16625200	Weak transcription	Ovary	ovary
9	chr9:16621400-16625400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:16622400-16626200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr9:16622400-16626600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr9:16622400-16628600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr9:16622400-16628600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr9:16622400-16628800	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr9:16622600-16626400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr9:16622600-16628600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr9:16623200-16625600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:16623200-16628000	Enhancers	Fetal Lung	lung
19	chr9:16623800-16626600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:16624000-16625200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:16624000-16625800	Enhancers	HSMMtube	muscle
22	chr9:16624000-16628200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:16624200-16625200	Enhancers	HUVEC	blood vessel
24	chr9:16624200-16626400	Enhancers	Rectal Smooth Muscle	rectum
25	chr9:16624200-16626400	Enhancers	NHDF-Ad	bronchial
26	chr9:16624200-16626600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:16624200-16627600	Enhancers	Dnd41	blood
28	chr9:16624200-16629000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:16624200-16629200	Enhancers	Fetal Stomach	stomach
30	chr9:16624200-16630400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:16624400-16625200	Enhancers	NHLF	lung
32	chr9:16624400-16625400	Enhancers	Colon Smooth Muscle	Colon
33	chr9:16624400-16626400	Enhancers	Stomach Smooth Muscle	stomach
34	chr9:16624400-16627800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:16624400-16628800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr9:16624600-16625600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:16624600-16625600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:16624600-16625800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr9:16624600-16628800	Enhancers	Fetal Kidney	kidney
40	chr9:16624800-16625200	Enhancers	Fetal Muscle Leg	muscle
41	chr9:16624800-16625400	Enhancers	Adipose Nuclei	Adipose
42	chr9:16624800-16625600	Enhancers	NH-A	brain
43	chr9:16624800-16626000	Enhancers	A549	lung
44	chr9:16624800-16626000	Enhancers	Osteobl	bone
45	chr9:16624800-16626600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:16624800-16628600	Enhancers	H1 Cell Line	embryonic stem cell
47	chr9:16624800-16628800	Enhancers	Fetal Thymus	thymus
48	chr9:16625000-16625200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr9:16625000-16626600	Enhancers	HSMM	muscle
50	chr9:16625000-16626800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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