Variant report

Variant	rs4949817
Chromosome Location	chr1:78070611-78070612
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78070290..78072373-chr1:78147292..78150145,3	K562	blood:
2	chr1:78065469..78069224-chr1:78069679..78073239,3	K562	blood:

Variant related genes	Relation type
ENSG00000036549	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1038983	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10873951	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs10873953	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10873954	0.81[AMR][1000 genomes]
rs11162366	0.89[ASN][1000 genomes]
rs11162368	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162374	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11162378	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11162380	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11162384	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11578805	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1166586	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1166589	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12026939	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12090729	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12132838	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12135104	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12142441	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12717768	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1389789	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1389790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1539739	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs166770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2031342	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs203229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2088058	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2296227	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs278832	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs278833	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278834	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278836	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278840	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278841	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs278842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278843	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278844	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs278848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278851	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs278855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278857	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278858	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278859	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278860	0.85[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278864	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs366467	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs370335	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3767037	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3767038	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4488068	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4949661	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949814	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4949818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs574973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6603956	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6603958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6603960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6657290	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6661656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6670660	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6672200	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6674638	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6687501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6691317	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6698151	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6699205	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6699311	1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs717333	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7519946	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7535781	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7536206	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7543037	0.82[EUR][1000 genomes]
rs7545175	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7546365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7552291	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7556523	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8179272	0.85[AMR][1000 genomes]
rs872342	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9662527	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9988619	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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
rs4949817	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78024800-78071000	Weak transcription	Gastric	stomach
2	chr1:78032600-78070800	Weak transcription	Aorta	Aorta
3	chr1:78033200-78072600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:78033600-78070800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:78038600-78071000	Weak transcription	Pancreas	Pancrea
6	chr1:78039000-78070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:78042000-78070800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:78042000-78074600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:78042200-78073800	Weak transcription	Fetal Brain Female	brain
10	chr1:78047000-78070800	Weak transcription	Lung	lung
11	chr1:78047000-78071200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:78047600-78070800	Weak transcription	HSMMtube	muscle
13	chr1:78047600-78071000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:78047600-78071600	Weak transcription	Thymus	Thymus
15	chr1:78047600-78072400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:78047600-78072600	Weak transcription	Fetal Kidney	kidney
17	chr1:78047600-78074600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:78047600-78074800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:78047600-78085600	Weak transcription	NHLF	lung
20	chr1:78047800-78070800	Weak transcription	Left Ventricle	heart
21	chr1:78047800-78070800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:78047800-78071000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:78047800-78074200	Weak transcription	Hela-S3	cervix
24	chr1:78047800-78074800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:78047800-78086200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:78047800-78090000	Weak transcription	NH-A	brain
27	chr1:78048000-78074600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:78048000-78077800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:78048000-78097400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:78048600-78070800	Weak transcription	Fetal Stomach	stomach
31	chr1:78048800-78070800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:78048800-78071000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:78048800-78071000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:78049000-78072400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:78050000-78075000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:78053600-78070800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:78054000-78074800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:78055400-78070800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:78056600-78074000	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:78057200-78070800	Weak transcription	Spleen	Spleen
41	chr1:78058000-78074800	Weak transcription	Brain Germinal Matrix	brain
42	chr1:78058200-78070800	Weak transcription	Psoas Muscle	Psoas
43	chr1:78059000-78083200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:78061000-78070800	Weak transcription	HUVEC	blood vessel
45	chr1:78061200-78070800	Weak transcription	NHEK	skin
46	chr1:78061200-78072400	Weak transcription	GM12878-XiMat	blood
47	chr1:78062800-78074200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:78063200-78070800	Weak transcription	Placenta	Placenta
49	chr1:78063200-78071000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:78063200-78083000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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