Variant report

Variant	rs59664047
Chromosome Location	chr2:96869291-96869292
allele	A/C
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	MXI1	chr2:96868951-96869417	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:96867904-96869365	HepG2	liver:	n/a	n/a
3	USF2	chr2:96869078-96869371	GM12878	blood:	n/a	n/a
4	IRF1	chr2:96869044-96869415	K562	blood:	n/a	chr2:96869167-96869180 chr2:96869169-96869179 chr2:96869120-96869136 chr2:96869167-96869180 chr2:96869170-96869181 chr2:96869117-96869130 chr2:96869169-96869180 chr2:96869201-96869211 chr2:96869165-96869179 chr2:96869167-96869180 chr2:96869166-96869180 chr2:96869169-96869183
5	ZNF263	chr2:96869162-96870132	HEK293-T-REx	kidney:	n/a	n/a
6	KAP1	chr2:96869105-96869963	HEK293	kidney:	n/a	n/a
7	POLR2A	chr2:96868838-96869520	K562	blood:	n/a	n/a
8	IRF3	chr2:96869271-96869405	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:96869174-96869431	K562	blood:	n/a	n/a
10	BHLHE40	chr2:96869172-96869298	GM12878	blood:	n/a	n/a
11	WRNIP1	chr2:96867922-96869943	GM12878	blood:	n/a	n/a
12	SMC3	chr2:96868896-96869307	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:96868962-96869334	GM12878	blood:	n/a	n/a
14	TBL1XR1	chr2:96868812-96869476	GM12878	blood:	n/a	n/a
15	ZNF384	chr2:96869206-96869339	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:96866562..96869403-chr2:96928080..96929883,2	K562	blood:
2	chr2:96849954..96852310-chr2:96867571..96870089,2	K562	blood:
3	chr2:96868913..96876440-chr2:96928017..96934530,23	K562	blood:

Variant related genes	Relation type
STARD7-AS1	TF binding region
ENSG00000135956	Chromatin interaction
ENSG00000144021	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11551400	0.86[EUR][1000 genomes]
rs12613263	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12617019	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12618133	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2276650	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3852673	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4371393	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4592891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4826	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57476471	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59082429	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60409279	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62152972	1.00[ASN][1000 genomes]
rs62153010	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62153011	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153014	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62153018	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153020	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62153022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153029	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6576968	0.95[ASN][1000 genomes]
rs6756208	0.98[ASN][1000 genomes]
rs72825854	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825856	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825877	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73958180	1.00[ASN][1000 genomes]
rs7579709	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7580178	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs997547	1.00[ASN][1000 genomes]
rs997548	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][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	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS 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	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3435047	chr2:96836850-96890437	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription 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 target site	37 gene(s)	inside rSNPs	diseases
8	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59664047	CIAO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96849600-96872600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:96849800-96871000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:96851000-96869400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:96859000-96870800	Weak transcription	Fetal Brain Male	brain
5	chr2:96859000-96870800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:96859000-96873200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:96860200-96869400	Weak transcription	Aorta	Aorta
8	chr2:96860200-96871200	Weak transcription	Fetal Kidney	kidney
9	chr2:96861000-96871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:96861200-96869600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:96861200-96869800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:96861400-96870000	Weak transcription	Fetal Brain Female	brain
13	chr2:96861400-96871000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:96861400-96872200	Weak transcription	Placenta	Placenta
15	chr2:96861400-96872800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:96861400-96872800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:96861600-96869400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:96861600-96869400	Weak transcription	Fetal Stomach	stomach
19	chr2:96861600-96870200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:96861800-96869800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:96861800-96870600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:96861800-96870800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:96862200-96869600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:96862200-96870600	Weak transcription	NH-A	brain
25	chr2:96863400-96869400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr2:96863800-96870200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:96864200-96870600	Enhancers	Brain Anterior Caudate	brain
28	chr2:96864200-96871800	Enhancers	Primary B cells from peripheral blood	blood
29	chr2:96864200-96872600	Enhancers	Brain Substantia Nigra	brain
30	chr2:96865200-96871200	Enhancers	Stomach Mucosa	stomach
31	chr2:96865400-96870600	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr2:96865600-96870800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:96865800-96869400	Genic enhancers	HepG2	liver
34	chr2:96865800-96869600	Enhancers	Psoas Muscle	Psoas
35	chr2:96866000-96870400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:96866200-96869400	Weak transcription	Lung	lung
37	chr2:96866200-96872800	Enhancers	Adipose Nuclei	Adipose
38	chr2:96866400-96872800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:96866800-96869600	Enhancers	Left Ventricle	heart
40	chr2:96866800-96869800	Weak transcription	Gastric	stomach
41	chr2:96867000-96870600	Enhancers	HMEC	breast
42	chr2:96867000-96872600	Enhancers	Fetal Muscle Leg	muscle
43	chr2:96867000-96873000	Enhancers	Small Intestine	intestine
44	chr2:96867200-96869800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr2:96867200-96870800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:96867600-96869400	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr2:96867600-96869400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:96867600-96870600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:96867600-96870800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr2:96867600-96870800	Enhancers	Brain Angular Gyrus	brain

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