Variant report

Variant	rs12652881
Chromosome Location	chr5:124258221-124258222
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10038794	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10041713	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10041724	0.88[ASN][1000 genomes]
rs10051446	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10055828	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10058365	0.92[ASN][1000 genomes]
rs10061263	0.80[ASN][1000 genomes]
rs10066786	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10070612	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10073890	0.80[ASN][1000 genomes]
rs10074013	0.80[ASN][1000 genomes]
rs10077638	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10078386	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1026010	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10463783	0.83[EUR][1000 genomes]
rs10478645	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10793807	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11241775	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11241776	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11241777	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11241779	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11743521	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11743554	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11951671	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11953197	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11958289	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12109265	0.82[ASN][1000 genomes]
rs12652556	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12652885	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12653706	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12654010	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12654041	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12654479	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12654486	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12654606	0.91[AMR][1000 genomes]
rs12654613	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12655869	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12655887	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12656060	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12656194	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12656225	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12657832	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12658154	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13359971	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1374130	0.81[ASN][1000 genomes]
rs17152193	0.82[ASN][1000 genomes]
rs2028854	0.80[ASN][1000 genomes]
rs28375332	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35862376	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36041674	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4240384	0.82[ASN][1000 genomes]
rs4279337	0.80[ASN][1000 genomes]
rs4311414	0.82[ASN][1000 genomes]
rs4331894	0.82[ASN][1000 genomes]
rs4836131	0.80[ASN][1000 genomes]
rs56110557	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59020249	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62370848	0.87[ASN][1000 genomes]
rs6869863	0.89[ASN][1000 genomes]
rs6875187	0.82[ASN][1000 genomes]
rs6875370	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6875763	0.82[ASN][1000 genomes]
rs6876036	0.81[ASN][1000 genomes]
rs6895658	0.89[ASN][1000 genomes]
rs6895765	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6898265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73782503	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7732618	0.82[ASN][1000 genomes]
rs9327340	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9968605	0.82[ASN][1000 genomes]

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	nsv882822	chr5:124250018-124449375	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124249400-124263200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:124251200-124259400	Enhancers	Dnd41	blood
3	chr5:124254000-124259800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:124254000-124260200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:124254200-124259200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr5:124254200-124259200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr5:124254200-124259400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr5:124254200-124259400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr5:124254200-124259600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:124254200-124259600	Enhancers	Brain Substantia Nigra	brain
11	chr5:124254200-124259800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:124254200-124259800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr5:124254200-124259800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr5:124254200-124259800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:124254200-124259800	Enhancers	Brain Hippocampus Middle	brain
16	chr5:124254200-124260400	Enhancers	Brain Cingulate Gyrus	brain
17	chr5:124254400-124259400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:124254400-124259600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr5:124254600-124260200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr5:124255200-124258800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:124255200-124259600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr5:124255600-124259400	Enhancers	Fetal Brain Female	brain
23	chr5:124256000-124258600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:124256200-124259600	Enhancers	Brain Angular Gyrus	brain
25	chr5:124257000-124258400	Weak transcription	Fetal Kidney	kidney
26	chr5:124257000-124259200	Enhancers	Fetal Brain Male	brain
27	chr5:124257200-124258800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:124257200-124259000	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr5:124257200-124259200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr5:124257200-124259200	Enhancers	Primary B cells from peripheral blood	blood
31	chr5:124257200-124259200	Flanking Active TSS	GM12878-XiMat	blood
32	chr5:124257200-124259600	Enhancers	Fetal Lung	lung
33	chr5:124257200-124260200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:124257400-124259600	Enhancers	Primary B cells from cord blood	blood
35	chr5:124257600-124259200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:124257600-124260200	Enhancers	Brain Germinal Matrix	brain
37	chr5:124257800-124258800	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr5:124257800-124259000	Enhancers	Duodenum Mucosa	Duodenum
39	chr5:124257800-124259200	Enhancers	Brain Anterior Caudate	brain
40	chr5:124257800-124259200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr5:124257800-124259400	Enhancers	H1 Cell Line	embryonic stem cell
42	chr5:124257800-124259400	Enhancers	Colon Smooth Muscle	Colon
43	chr5:124258000-124258800	Enhancers	Fetal Intestine Small	intestine
44	chr5:124258000-124259200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr5:124258000-124259200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr5:124258000-124259400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr5:124258000-124259800	Enhancers	Fetal Stomach	stomach
48	chr5:124258200-124258600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr5:124258200-124259000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr5:124258200-124259200	Enhancers	Stomach Mucosa	stomach

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