Variant report

Variant	rs4671242
Chromosome Location	chr2:55410664-55410665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10172326	0.93[CEU][hapmap];0.91[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10193022	0.82[AFR][1000 genomes]
rs10197309	0.88[AMR][1000 genomes]
rs1133181	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679663	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685292	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12616435	0.82[ASN][1000 genomes]
rs12621144	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13012766	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13013134	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13019355	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13021215	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13023235	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13417057	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs14026	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1437391	0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[YRI][hapmap]
rs2164714	0.87[CEU][hapmap];0.82[ASN][1000 genomes]
rs2576710	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2576724	0.81[ASN][1000 genomes]
rs2864818	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34054131	0.83[ASN][1000 genomes]
rs34564471	0.92[ASN][1000 genomes]
rs35026006	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35161040	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35890669	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762509	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3935223	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4420737	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671241	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672024	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4672025	0.84[ASN][1000 genomes]
rs4672026	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4672027	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56095114	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs56339196	0.82[ASN][1000 genomes]
rs6545474	0.93[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545475	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs6545478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714830	0.93[CEU][hapmap];0.96[CHB][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6715130	0.82[ASN][1000 genomes]
rs6759911	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7595134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4671242	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
2	chr2:55393000-55422000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:55394000-55419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:55395600-55412400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:55395600-55422800	Weak transcription	Ovary	ovary
6	chr2:55395600-55427000	Weak transcription	Left Ventricle	heart
7	chr2:55395800-55418200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:55395800-55418400	Weak transcription	Fetal Intestine Large	intestine
9	chr2:55395800-55427000	Weak transcription	Aorta	Aorta
10	chr2:55397200-55450000	Weak transcription	NH-A	brain
11	chr2:55397400-55411600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:55397400-55422400	Weak transcription	HSMMtube	muscle
13	chr2:55397400-55423000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:55399600-55419000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:55399600-55423000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:55399800-55416600	Weak transcription	Primary T cells from cord blood	blood
17	chr2:55401600-55419000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:55402600-55422000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:55402600-55423200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:55402800-55450000	Weak transcription	NHDF-Ad	bronchial
21	chr2:55403200-55423800	Weak transcription	Osteobl	bone
22	chr2:55403200-55426800	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:55403200-55431800	Weak transcription	Fetal Brain Male	brain
24	chr2:55403400-55418800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:55403400-55423000	Weak transcription	NHEK	skin
26	chr2:55403600-55416600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:55403600-55420600	Weak transcription	HSMM	muscle
28	chr2:55404200-55423000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:55405400-55423000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:55406800-55423000	Weak transcription	Lung	lung
31	chr2:55408600-55423000	Weak transcription	Pancreas	Pancrea
32	chr2:55408800-55423600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:55409000-55423000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:55409200-55416600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:55409200-55425800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:55409400-55412400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:55409400-55418400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:55409600-55418400	Weak transcription	Fetal Stomach	stomach
39	chr2:55409800-55418200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:55410000-55411200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:55410000-55424000	Weak transcription	Fetal Thymus	thymus
42	chr2:55410600-55411200	Weak transcription	Fetal Intestine Small	intestine
43	chr2:55410600-55422800	Weak transcription	HepG2	liver

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