Variant report

Variant	rs8006657
Chromosome Location	chr14:55245149-55245150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55013489..55016252-chr14:55244826..55246985,2	K562	blood:
2	chr14:55165172..55166769-chr14:55243179..55246172,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10136563	0.94[ASN][1000 genomes]
rs10138916	0.94[ASN][1000 genomes]
rs1040877	0.95[ASN][1000 genomes]
rs1114050	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1114051	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11158024	0.84[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs11431	0.81[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs12586289	0.84[ASN][1000 genomes]
rs12886870	0.93[ASN][1000 genomes]
rs12887011	0.93[ASN][1000 genomes]
rs2181049	0.95[ASN][1000 genomes]
rs2281650	0.92[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2281652	1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2295824	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3813402	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4402472	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4409990	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4506812	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4508355	0.94[ASN][1000 genomes]
rs4516125	0.94[ASN][1000 genomes]
rs4901541	0.85[JPT][hapmap]
rs4901542	0.82[JPT][hapmap];0.87[YRI][hapmap]
rs4901547	0.92[ASN][1000 genomes]
rs6572975	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs6572976	0.95[ASN][1000 genomes]
rs6572977	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6572978	0.93[ASN][1000 genomes]
rs6572980	0.94[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs709939	0.91[JPT][hapmap];0.96[MEX][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7143189	0.82[JPT][hapmap]
rs7148657	0.94[ASN][1000 genomes]
rs7150628	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7151853	0.94[ASN][1000 genomes]
rs7153975	0.94[ASN][1000 genomes]
rs7155922	0.82[JPT][hapmap]
rs7158665	0.82[JPT][hapmap]
rs8011598	0.94[ASN][1000 genomes]
rs8011837	0.93[ASN][1000 genomes]
rs8011848	0.93[ASN][1000 genomes]
rs8013211	0.93[ASN][1000 genomes]
rs8021151	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[ASN][1000 genomes]
rs8021325	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8021957	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs8022503	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs911614	0.82[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs911615	0.95[ASN][1000 genomes]
rs927379	0.94[ASN][1000 genomes]
rs927380	0.94[ASN][1000 genomes]
rs927381	0.94[ASN][1000 genomes]
rs927382	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[ASN][1000 genomes]
rs927383	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs971256	0.88[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530042	chr14:55208170-55386966	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8006657	RPL13AP3	cis	parietal	SCAN
rs8006657	KTN1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55231800-55245400	Weak transcription	Pancreas	Pancrea
2	chr14:55236600-55245400	Genic enhancers	Fetal Muscle Leg	muscle
3	chr14:55237600-55261200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr14:55238200-55245200	Enhancers	Fetal Heart	heart
5	chr14:55240000-55250400	Strong transcription	HepG2	liver
6	chr14:55240600-55251200	Weak transcription	Gastric	stomach
7	chr14:55240600-55253600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr14:55240600-55254800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:55240600-55257000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr14:55240800-55245600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr14:55240800-55250000	Weak transcription	Colonic Mucosa	Colon
12	chr14:55240800-55250800	Weak transcription	Esophagus	oesophagus
13	chr14:55240800-55253800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr14:55240800-55256000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr14:55240800-55256400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:55240800-55256400	Weak transcription	Brain Angular Gyrus	brain
17	chr14:55240800-55259200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr14:55240800-55261600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr14:55240800-55261600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr14:55241000-55245600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr14:55241000-55249200	Weak transcription	Right Atrium	heart
22	chr14:55241000-55256400	Weak transcription	Ovary	ovary
23	chr14:55241000-55258400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr14:55241000-55259200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr14:55241000-55260200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr14:55241000-55263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr14:55241200-55257600	Weak transcription	K562	blood
28	chr14:55241200-55272200	Weak transcription	A549	lung
29	chr14:55241600-55248600	Strong transcription	Fetal Intestine Large	intestine
30	chr14:55241600-55248600	Strong transcription	Fetal Intestine Small	intestine
31	chr14:55241800-55245800	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr14:55241800-55246000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
33	chr14:55241800-55249000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr14:55241800-55257400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr14:55242400-55245800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr14:55242400-55246400	Enhancers	Liver	Liver
37	chr14:55243000-55245400	Weak transcription	Spleen	Spleen
38	chr14:55243000-55246800	Strong transcription	Placenta	Placenta
39	chr14:55243200-55249200	Strong transcription	Left Ventricle	heart
40	chr14:55243400-55246000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr14:55243400-55247800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr14:55243400-55251000	Weak transcription	Brain Substantia Nigra	brain
43	chr14:55243400-55253800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr14:55243400-55256000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr14:55243600-55247200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr14:55243600-55249200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr14:55243600-55250000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr14:55243600-55250800	Strong transcription	Colon Smooth Muscle	Colon
49	chr14:55243600-55251000	Weak transcription	Brain Anterior Caudate	brain
50	chr14:55243600-55253600	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links