Variant report

Variant	rs4839602
Chromosome Location	chr3:143297057-143297058
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	chr3:143296828..143299169-chr3:143301224..143303215,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10513212	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs11719391	0.94[ASN][1000 genomes]
rs12494880	0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs13061355	1.00[ASW][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs13061398	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13064748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068070	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13069703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13071089	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13074668	0.84[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13074737	0.84[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13076528	0.81[JPT][hapmap]
rs13076949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084941	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs13085205	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13090915	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1405017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525862	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1525863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16853857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17640925	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1880662	1.00[ASW][hapmap]
rs1983467	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2030818	0.83[CHB][hapmap]
rs2289451	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35417581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35593863	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4839601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839603	0.92[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4839642	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4839646	0.81[ASN][1000 genomes]
rs71307941	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71307942	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs746055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642430	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs9841219	1.00[ASW][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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv829745	chr3:143278512-143405626	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4839602	TFDP2	cis	cerebellum	SCAN
rs4839602	GK5	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143256000-143305600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:143270600-143304800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:143277400-143301200	Weak transcription	Esophagus	oesophagus
4	chr3:143277400-143303600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:143277400-143310200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:143284000-143306400	Weak transcription	Spleen	Spleen
7	chr3:143284400-143299200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:143285000-143300400	Weak transcription	Brain Anterior Caudate	brain
9	chr3:143286800-143298000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:143286800-143300400	Weak transcription	GM12878-XiMat	blood
11	chr3:143286800-143302000	Weak transcription	Brain Angular Gyrus	brain
12	chr3:143286800-143304400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:143286800-143304800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:143287000-143297600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:143287000-143305000	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:143287200-143297400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:143287400-143304800	Weak transcription	Fetal Intestine Small	intestine
18	chr3:143289400-143303000	Weak transcription	Fetal Stomach	stomach
19	chr3:143289600-143304600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:143290600-143302400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:143290600-143304600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:143291000-143301400	Weak transcription	Lung	lung
23	chr3:143291000-143303600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:143291000-143304600	Weak transcription	Adipose Nuclei	Adipose
25	chr3:143291200-143305000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:143291600-143301400	Weak transcription	Placenta	Placenta
27	chr3:143291600-143305000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:143292400-143305400	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:143292600-143297200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:143293000-143304800	Weak transcription	Aorta	Aorta
31	chr3:143293600-143301000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:143294200-143304800	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:143294400-143317800	Weak transcription	Brain Substantia Nigra	brain
34	chr3:143294800-143298800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:143294800-143309400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:143295000-143297800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:143295200-143297600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:143295200-143300400	Strong transcription	Primary T cells from cord blood	blood
39	chr3:143295400-143297400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:143295600-143297600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr3:143295600-143301200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr3:143295800-143302600	Weak transcription	Fetal Lung	lung
43	chr3:143296200-143297600	Strong transcription	Primary B cells from cord blood	blood
44	chr3:143296200-143313200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:143296400-143297600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr3:143296400-143297800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr3:143296600-143299400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:143296800-143304000	Weak transcription	Ovary	ovary
49	chr3:143297000-143298600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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