Variant report

Variant	rs4949814
Chromosome Location	chr1:78036688-78036689
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78030983..78033542-chr1:78034721..78037146,2	K562	blood:

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1038983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10873955	0.81[EUR][1000 genomes]
rs11162365	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11162366	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11162368	0.92[ASN][1000 genomes]
rs11162369	0.85[EUR][1000 genomes]
rs11162370	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11162372	0.87[EUR][1000 genomes]
rs11162374	0.80[ASN][1000 genomes]
rs11162378	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11162380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs11162383	0.81[EUR][1000 genomes]
rs11162386	0.82[EUR][1000 genomes]
rs11162387	0.81[EUR][1000 genomes]
rs11578805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs12026939	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12074409	0.81[YRI][hapmap]
rs12132838	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12142671	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs12717767	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12717768	0.96[ASN][1000 genomes]
rs1389789	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1389790	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1565850	0.81[YRI][hapmap]
rs1565851	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1565852	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs166770	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1962523	0.89[AMR][1000 genomes]
rs203229	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2088058	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2296227	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs278833	0.91[EUR][1000 genomes]
rs278834	0.84[ASN][1000 genomes]
rs278836	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278837	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs278842	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs278843	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278847	0.82[EUR][1000 genomes]
rs278848	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs278850	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs278851	0.80[ASN][1000 genomes]
rs278854	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs278855	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs278856	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs278857	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278860	0.82[CEU][hapmap];0.84[ASN][1000 genomes]
rs278863	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs278864	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3509	0.86[AMR][1000 genomes]
rs366467	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs370335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs371076	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs3767037	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs3767038	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4245658	0.82[YRI][hapmap]
rs4589153	0.81[YRI][hapmap]
rs4600093	0.81[YRI][hapmap]
rs4949658	0.81[YRI][hapmap]
rs4949661	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949816	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4949817	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4949818	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4949822	0.81[EUR][1000 genomes]
rs56688304	0.81[EUR][1000 genomes]
rs574973	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6603955	0.84[EUR][1000 genomes]
rs6603956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6603958	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6603960	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6657290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6661656	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6670660	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6672200	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs6674638	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6687501	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6687596	0.81[EUR][1000 genomes]
rs6691317	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695989	0.81[YRI][hapmap]
rs6698151	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6699205	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6699311	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs717333	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs728741	0.89[AMR][1000 genomes]
rs7521042	0.84[EUR][1000 genomes]
rs7524866	0.93[CEU][hapmap];0.83[AMR][1000 genomes]
rs7535781	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7545175	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7545544	0.81[YRI][hapmap]
rs7546365	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7552291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556227	0.82[EUR][1000 genomes]
rs7556523	0.84[ASN][1000 genomes]
rs872342	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs962388	0.84[AMR][1000 genomes]
rs9662527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs9988619	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4949814	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78006200-78064400	Weak transcription	Stomach Mucosa	stomach
2	chr1:78023200-78050200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:78023400-78046200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:78023800-78048800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:78024600-78048000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:78024800-78038000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:78024800-78038000	Weak transcription	Pancreas	Pancrea
8	chr1:78024800-78048400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:78024800-78071000	Weak transcription	Gastric	stomach
10	chr1:78025000-78038000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:78025400-78050600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:78026000-78049400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr1:78026400-78048800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:78026800-78049200	Weak transcription	Colonic Mucosa	Colon
15	chr1:78027200-78049800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:78028600-78054600	Weak transcription	Esophagus	oesophagus
17	chr1:78029400-78039800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:78029800-78038000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:78029800-78047800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:78029800-78048000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:78029800-78050600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:78030000-78048800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:78030200-78048200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr1:78030200-78048800	Strong transcription	Fetal Intestine Large	intestine
25	chr1:78030200-78049400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:78030400-78039200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:78030400-78047600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr1:78030400-78050400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:78030600-78038800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:78030600-78047800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:78031000-78039000	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:78031000-78039200	Strong transcription	Fetal Muscle Leg	muscle
33	chr1:78031600-78041800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:78032000-78047200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:78032000-78049000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:78032000-78062800	Weak transcription	Fetal Heart	heart
37	chr1:78032400-78047000	Weak transcription	Fetal Brain Male	brain
38	chr1:78032600-78046600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr1:78032600-78070800	Weak transcription	Aorta	Aorta
40	chr1:78032800-78038000	Weak transcription	Fetal Stomach	stomach
41	chr1:78032800-78041000	Weak transcription	Brain Germinal Matrix	brain
42	chr1:78032800-78070600	Weak transcription	Small Intestine	intestine
43	chr1:78033000-78037200	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:78033000-78040200	Weak transcription	Ovary	ovary
45	chr1:78033000-78057000	Weak transcription	Spleen	Spleen
46	chr1:78033000-78057200	Weak transcription	Psoas Muscle	Psoas
47	chr1:78033200-78037200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:78033200-78038000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:78033200-78038200	Weak transcription	Thymus	Thymus
50	chr1:78033200-78043200	Weak transcription	Lung	lung

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