Variant report

Variant	rs1995529
Chromosome Location	chr3:143564093-143564094
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10433436	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10513218	1.00[CHB][hapmap]
rs11714060	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319100	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319101	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1394398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394402	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1504603	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1504604	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1504605	1.00[GIH][hapmap]
rs16834862	1.00[GIH][hapmap]
rs16854543	1.00[GIH][hapmap]
rs1979911	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1995530	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011290	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2011297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2011303	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2361202	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2361203	0.94[EUR][1000 genomes]
rs2361205	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2361206	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2361207	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2361208	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2361209	1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2885193	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2885194	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2885195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4286430	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4499594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839612	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4839671	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs4839672	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4839673	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4839674	1.00[CEU][hapmap]
rs56220620	1.00[ASN][1000 genomes]
rs56407400	1.00[ASN][1000 genomes]
rs57718888	1.00[ASN][1000 genomes]
rs58887384	1.00[ASN][1000 genomes]
rs58921154	1.00[ASN][1000 genomes]
rs59306133	1.00[ASN][1000 genomes]
rs60249173	0.85[ASN][1000 genomes]
rs60523819	1.00[ASN][1000 genomes]
rs60550983	0.85[ASN][1000 genomes]
rs6440195	1.00[CEU][hapmap]
rs6440196	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6768399	1.00[CHB][hapmap]
rs6768702	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6780027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6782974	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs6794907	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73869037	0.85[ASN][1000 genomes]
rs73869039	0.85[ASN][1000 genomes]
rs73869041	0.85[ASN][1000 genomes]
rs73869042	1.00[ASN][1000 genomes]
rs73869048	1.00[ASN][1000 genomes]
rs73869049	1.00[ASN][1000 genomes]
rs73869050	1.00[ASN][1000 genomes]
rs73871822	1.00[ASN][1000 genomes]
rs73871823	1.00[ASN][1000 genomes]
rs73871826	1.00[ASN][1000 genomes]
rs73871827	1.00[ASN][1000 genomes]
rs7434217	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7613146	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7623477	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7624170	1.00[GIH][hapmap]
rs7627020	1.00[EUR][1000 genomes]
rs7629598	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637640	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7645681	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7653164	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap]
rs9289669	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9824974	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9847107	1.00[GIH][hapmap]
rs9870661	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][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	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	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1995529	C14orf143	trans	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143541400-143565200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:143545600-143565400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:143549200-143565200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:143549400-143565000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:143550000-143565200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:143551400-143565800	Weak transcription	Adipose Nuclei	Adipose
7	chr3:143554200-143565800	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:143555400-143564200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:143558400-143566600	Weak transcription	Esophagus	oesophagus
10	chr3:143558600-143566000	Weak transcription	Ovary	ovary
11	chr3:143559800-143565800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:143559800-143566400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:143559800-143566400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:143560200-143564400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:143560200-143565200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:143560200-143565800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:143560200-143566600	Weak transcription	Small Intestine	intestine
18	chr3:143561400-143565800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:143561800-143564200	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:143561800-143564400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:143562000-143564400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:143562000-143564800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:143562000-143565800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:143562200-143566600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:143562400-143565200	Enhancers	Brain Hippocampus Middle	brain
26	chr3:143562400-143565800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:143563200-143567600	Active TSS	GM12878-XiMat	blood
28	chr3:143563600-143565800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr3:143563600-143565800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr3:143563800-143564200	Weak transcription	Primary B cells from cord blood	blood
31	chr3:143563800-143564400	Weak transcription	Fetal Stomach	stomach
32	chr3:143563800-143564600	Active TSS	Brain Anterior Caudate	brain
33	chr3:143563800-143564800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr3:143563800-143565800	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr3:143563800-143565800	Enhancers	Brain Cingulate Gyrus	brain
36	chr3:143563800-143565800	Enhancers	Brain Substantia Nigra	brain
37	chr3:143563800-143566400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr3:143564000-143564200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:143564000-143564200	Enhancers	Brain Angular Gyrus	brain
40	chr3:143564000-143564600	Enhancers	Fetal Lung	lung
41	chr3:143564000-143565000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:143564000-143566000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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