Variant report

Variant	rs2281652
Chromosome Location	chr14:55253864-55253865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55031208..55035304-chr14:55253192..55258095,4	K562	blood:
2	chr14:55031577..55034283-chr14:55252159..55255561,3	MCF-7	breast:
3	chr14:55030029..55031723-chr14:55251131..55254123,2	K562	blood:
4	chr14:55252117..55254056-chr14:55258046..55260281,2	K562	blood:
5	chr14:55048694..55051094-chr14:55253283..55255038,2	K562	blood:

Variant related genes	Relation type
ENSG00000020577	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10136563	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10138916	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1040877	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1114050	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1114051	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11158024	0.95[JPT][hapmap]
rs11431	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12586289	0.95[EUR][1000 genomes]
rs12886870	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12887011	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2181049	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2281650	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281653	0.92[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs2295824	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs3813402	0.84[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4402472	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4409990	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4506812	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4508355	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4511452	0.83[EUR][1000 genomes]
rs4516125	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4898855	0.82[EUR][1000 genomes]
rs4901541	0.85[JPT][hapmap]
rs4901542	0.84[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs4901547	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4901548	0.81[CEU][hapmap]
rs6572975	0.96[CEU][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs6572976	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6572977	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6572978	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6572980	0.88[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs709939	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7143189	0.84[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7148657	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7150498	0.88[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs7150628	0.96[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs7151853	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7153975	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7155922	0.84[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7158665	0.82[JPT][hapmap]
rs8006657	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]
rs8011598	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8011837	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8011848	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8013211	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8021151	0.83[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8021325	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8021957	0.96[CEU][hapmap];0.84[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8022503	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs911614	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs911615	0.90[ASN][1000 genomes]
rs927379	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs927380	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs927381	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs927382	0.83[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs927383	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs971256	0.80[CEU][hapmap]

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	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
2	esv1004703	chr14:55252382-55256132	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2281652	RPL13AP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55237600-55261200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr14:55240600-55254800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:55240600-55257000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr14:55240800-55256000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr14:55240800-55256400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr14:55240800-55256400	Weak transcription	Brain Angular Gyrus	brain
7	chr14:55240800-55259200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr14:55240800-55261600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr14:55240800-55261600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr14:55241000-55256400	Weak transcription	Ovary	ovary
11	chr14:55241000-55258400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr14:55241000-55259200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr14:55241000-55260200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr14:55241000-55263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr14:55241200-55257600	Weak transcription	K562	blood
16	chr14:55241200-55272200	Weak transcription	A549	lung
17	chr14:55241800-55257400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr14:55243400-55256000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr14:55243600-55261400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr14:55243800-55257400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr14:55243800-55258000	Strong transcription	HUVEC	blood vessel
22	chr14:55244000-55257400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr14:55244000-55257400	Strong transcription	NHEK	skin
24	chr14:55244000-55258200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr14:55244200-55257800	Strong transcription	HSMMtube	muscle
26	chr14:55244200-55258000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr14:55244200-55258200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr14:55244400-55256400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr14:55244400-55259400	Strong transcription	NHLF	lung
30	chr14:55244800-55257800	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr14:55245800-55257400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr14:55246600-55259400	Strong transcription	NHDF-Ad	bronchial
33	chr14:55247000-55257600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr14:55247200-55258000	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr14:55248600-55254800	Genic enhancers	Fetal Intestine Small	intestine
36	chr14:55249600-55255000	Genic enhancers	Fetal Muscle Leg	muscle
37	chr14:55249800-55255200	Weak transcription	Brain Hippocampus Middle	brain
38	chr14:55250000-55258000	Strong transcription	Rectal Smooth Muscle	rectum
39	chr14:55250000-55258800	Weak transcription	Primary B cells from cord blood	blood
40	chr14:55250200-55255400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr14:55250400-55257800	Strong transcription	Fetal Stomach	stomach
42	chr14:55250600-55258600	Weak transcription	Colonic Mucosa	Colon
43	chr14:55250600-55259000	Strong transcription	Adipose Nuclei	Adipose
44	chr14:55250600-55259000	Weak transcription	Fetal Lung	lung
45	chr14:55250800-55258000	Strong transcription	HepG2	liver
46	chr14:55251000-55254000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr14:55251000-55254200	Strong transcription	Placenta	Placenta
48	chr14:55251000-55257200	Weak transcription	Esophagus	oesophagus
49	chr14:55251000-55258000	Strong transcription	Stomach Smooth Muscle	stomach
50	chr14:55251400-55254200	Enhancers	Brain Substantia Nigra	brain

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