Variant report

Variant	rs1823220
Chromosome Location	chr3:143539799-143539800
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	chr3:143534241..143536547-chr3:143539436..143542162,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10433437	0.90[CHB][hapmap]
rs10513230	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10513231	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs10513232	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11920369	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12497227	0.90[CHB][hapmap]
rs1394403	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1504605	0.85[JPT][hapmap]
rs16854417	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16854421	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16854423	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16854424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16854463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16854493	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16854503	0.90[CHB][hapmap]
rs16854525	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17275413	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1900643	0.90[CHB][hapmap]
rs1900644	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1989180	0.90[CHB][hapmap]
rs2121774	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2361199	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2361204	0.90[CHB][hapmap]
rs4593022	1.00[EUR][1000 genomes]
rs4839612	1.00[CEU][hapmap]
rs4839613	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4839614	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4839659	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4839660	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4839661	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4839662	1.00[ASN][1000 genomes]
rs4839663	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4839670	0.90[CHB][hapmap]
rs55904283	0.98[ASN][1000 genomes]
rs56010653	0.98[ASN][1000 genomes]
rs62268898	1.00[ASN][1000 genomes]
rs6440202	0.85[JPT][hapmap]
rs6764661	0.90[CHB][hapmap]
rs6765414	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6769847	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6773087	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6776336	0.90[CHB][hapmap]
rs6792031	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6793658	1.00[ASN][1000 genomes]
rs6799226	0.82[JPT][hapmap]
rs6804065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997316	0.98[ASN][1000 genomes]
rs72997334	0.98[ASN][1000 genomes]
rs73008747	0.81[ASN][1000 genomes]
rs7621206	0.90[CHB][hapmap]
rs7651412	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7652644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs924851	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs951594	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs951595	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9822158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827103	0.90[CHB][hapmap]
rs9832471	0.90[CHB][hapmap]
rs9844917	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9847107	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv3418674	chr3:143457005-143558357	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	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
4	nsv1001076	chr3:143513526-143547076	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv536747	chr3:143513526-143547076	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1823220	C14orf143	trans	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143514200-143544200	Weak transcription	Primary T cells from cord blood	blood
2	chr3:143529600-143540600	Weak transcription	Brain Angular Gyrus	brain
3	chr3:143529600-143543800	Weak transcription	Stomach Mucosa	stomach
4	chr3:143530600-143539800	Weak transcription	Ovary	ovary
5	chr3:143530600-143540600	Weak transcription	Placenta	Placenta
6	chr3:143530800-143540800	Weak transcription	Fetal Stomach	stomach
7	chr3:143531000-143539800	Weak transcription	Adipose Nuclei	Adipose
8	chr3:143531000-143543200	Weak transcription	NHDF-Ad	bronchial
9	chr3:143531800-143543200	Weak transcription	Aorta	Aorta
10	chr3:143533600-143543200	Weak transcription	Fetal Lung	lung
11	chr3:143533800-143540600	Weak transcription	Primary B cells from cord blood	blood
12	chr3:143533800-143543200	Weak transcription	Right Atrium	heart
13	chr3:143534000-143539800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:143534000-143540600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:143534200-143539800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:143534200-143540000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:143534400-143539800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:143534400-143540600	Weak transcription	Fetal Thymus	thymus
19	chr3:143536000-143545200	Weak transcription	Gastric	stomach
20	chr3:143538000-143542200	Enhancers	Brain Substantia Nigra	brain
21	chr3:143538400-143539800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr3:143538600-143542000	Enhancers	Brain Cingulate Gyrus	brain
23	chr3:143538800-143541800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr3:143539000-143539800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr3:143539000-143540000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:143539000-143542200	Enhancers	Brain Hippocampus Middle	brain
27	chr3:143539200-143539800	Enhancers	Brain Anterior Caudate	brain
28	chr3:143539200-143540000	Enhancers	HSMM	muscle
29	chr3:143539200-143540200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:143539200-143540200	Enhancers	HSMMtube	muscle
31	chr3:143539200-143544600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr3:143539400-143540000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr3:143539400-143540000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr3:143539400-143540000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:143539400-143540200	Enhancers	Lung	lung
36	chr3:143539400-143541400	Enhancers	Spleen	Spleen
37	chr3:143539400-143541800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr3:143539400-143541800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:143539400-143545000	Weak transcription	Liver	Liver
40	chr3:143539600-143540600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:143539600-143540600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:143539600-143541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:143539600-143541400	Enhancers	Primary hematopoietic stem cells	blood
44	chr3:143539600-143541800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:143539600-143546600	Weak transcription	Esophagus	oesophagus
46	chr3:143539600-143550000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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