Variant report

Variant	rs2702332
Chromosome Location	chr4:56916879-56916880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56914879..56917642-chr4:56927334..56929102,2	MCF-7	breast:
2	chr4:56914423..56917343-chr4:56954991..56956586,2	MCF-7	breast:
3	chr4:56906651..56909346-chr4:56915136..56917400,3	MCF-7	breast:
4	chr4:56915544..56917169-chr4:56971414..56974217,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1108947	0.94[EUR][1000 genomes]
rs1108948	0.94[EUR][1000 genomes]
rs11721368	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11729231	0.80[EUR][1000 genomes]
rs11934389	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11938852	0.90[EUR][1000 genomes]
rs13102087	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13109242	0.81[EUR][1000 genomes]
rs13113844	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13121092	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13139132	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13147381	0.94[EUR][1000 genomes]
rs17086249	0.89[EUR][1000 genomes]
rs2412717	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2412718	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2412719	0.92[EUR][1000 genomes]
rs2412721	0.89[EUR][1000 genomes]
rs2412726	0.90[EUR][1000 genomes]
rs2412728	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2611818	0.81[EUR][1000 genomes]
rs2899054	0.90[EUR][1000 genomes]
rs34181414	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34683632	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34796075	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35400594	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35417087	0.91[EUR][1000 genomes]
rs35736349	0.80[EUR][1000 genomes]
rs35770075	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35786306	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35786805	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35976456	0.88[EUR][1000 genomes]
rs4364320	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58795379	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6554328	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6810857	0.84[EUR][1000 genomes]
rs6819574	0.83[EUR][1000 genomes]
rs6836376	0.87[EUR][1000 genomes]
rs6839220	0.93[EUR][1000 genomes]
rs6839870	0.88[EUR][1000 genomes]
rs71601617	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7657181	0.91[EUR][1000 genomes]
rs7659694	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7663270	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7672541	0.89[EUR][1000 genomes]
rs7676365	0.85[EUR][1000 genomes]
rs7685766	0.92[EUR][1000 genomes]

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	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2702332	KIAA1211	Cis_1M	lymphoblastoid	RTeQTL
rs2702332	CLOCK	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56914000-56917000	Active TSS	Cortex derived primary cultured neurospheres	brain
2	chr4:56914000-56917200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr4:56914200-56917000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:56914200-56917200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:56914200-56917400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:56914400-56917000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr4:56914400-56917200	Active TSS	Brain Substantia Nigra	brain
8	chr4:56914400-56917400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr4:56914400-56917800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:56914600-56917000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:56914600-56917000	Active TSS	Fetal Intestine Large	intestine
12	chr4:56914600-56917000	Active TSS	Fetal Kidney	kidney
13	chr4:56914800-56917000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr4:56914800-56917200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:56914800-56919600	Active TSS	Fetal Brain Female	brain
16	chr4:56915200-56917200	Active TSS	Primary hematopoietic stem cells	blood
17	chr4:56915800-56917200	Active TSS	Fetal Brain Male	brain
18	chr4:56916200-56917000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
19	chr4:56916200-56917200	Active TSS	Duodenum Mucosa	Duodenum
20	chr4:56916400-56917200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:56916400-56917400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:56916400-56919800	Active TSS	Brain Germinal Matrix	brain
23	chr4:56916400-56936200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:56916600-56917000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:56916600-56917200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:56916600-56917200	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr4:56916600-56917200	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr4:56916600-56917200	Enhancers	HepG2	liver
29	chr4:56916600-56917600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr4:56916600-56917600	Weak transcription	Fetal Heart	heart
31	chr4:56916600-56918600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:56916600-56921200	Weak transcription	Fetal Intestine Small	intestine
33	chr4:56916600-56921400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:56916600-56921600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:56916600-56929400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:56916600-56931600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:56916600-56934200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:56916800-56917000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr4:56916800-56917000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr4:56916800-56917000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr4:56916800-56917200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr4:56916800-56917200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:56916800-56917400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr4:56916800-56917400	Enhancers	Hela-S3	cervix
45	chr4:56916800-56917600	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr4:56916800-56921400	Weak transcription	H1 Cell Line	embryonic stem cell

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