Variant report

Variant	rs7519946
Chromosome Location	chr1:78217519-78217520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:78215450..78218218-chr1:78221700..78223456,2	MCF-7	breast:
2	chr1:78216628..78219981-chr1:78220321..78224068,4	K562	blood:
3	chr1:78216628..78222015-chr1:78222062..78227240,9	K562	blood:
4	chr1:78215243..78217892-chr1:78468395..78470149,2	K562	blood:
5	chr1:78213808..78218227-chr1:78468436..78472020,4	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM73A-1	chr1:78217436-78217681	expReg_chr1_10783_+

No data

Variant related genes	Relation type
ENSG00000077254	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10873953	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873954	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10873955	0.84[ASN][1000 genomes]
rs11162368	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11162370	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11162374	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11162378	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11162380	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162383	0.82[ASN][1000 genomes]
rs11162384	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11162386	0.84[ASN][1000 genomes]
rs11162387	0.84[ASN][1000 genomes]
rs11578805	0.91[ASN][1000 genomes]
rs1166586	0.85[ASN][1000 genomes]
rs1166589	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12090729	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12132838	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135104	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12142441	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12717768	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1389789	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1389790	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1539739	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs166770	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2031342	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203229	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2296227	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs278832	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs278833	0.84[ASN][1000 genomes]
rs278834	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278837	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs278840	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278841	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs278842	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278843	0.84[ASN][1000 genomes]
rs278844	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278848	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs278850	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs278851	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs278855	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs278856	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs278857	0.82[ASN][1000 genomes]
rs278858	0.82[ASN][1000 genomes]
rs278859	0.82[ASN][1000 genomes]
rs278860	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs278863	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs278864	0.82[ASN][1000 genomes]
rs3767037	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3767038	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4488068	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949817	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4949818	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4949822	0.84[ASN][1000 genomes]
rs56688304	0.99[ASN][1000 genomes]
rs574973	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6603958	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6603960	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6661656	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6672200	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687501	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6687596	0.99[ASN][1000 genomes]
rs6699205	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6699311	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs717333	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535781	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536206	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7543037	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7543125	0.84[ASN][1000 genomes]
rs7546365	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7556227	0.84[ASN][1000 genomes]
rs7556523	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8179272	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs872342	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9662527	0.89[ASN][1000 genomes]
rs9988619	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
5	esv1796958	chr1:78138955-78267421	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1798160	chr1:78149941-78267421	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	nsv508326	chr1:78184379-78234247	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7519946	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78173800-78224400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:78192200-78222400	Weak transcription	Brain Substantia Nigra	brain
3	chr1:78193000-78221200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:78193600-78222600	Weak transcription	Fetal Kidney	kidney
5	chr1:78194400-78223400	Weak transcription	NH-A	brain
6	chr1:78195400-78222200	Weak transcription	Gastric	stomach
7	chr1:78195400-78223200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:78195400-78224200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:78195400-78224800	Weak transcription	Spleen	Spleen
10	chr1:78196800-78221800	Weak transcription	Ovary	ovary
11	chr1:78197800-78221800	Weak transcription	Thymus	Thymus
12	chr1:78197800-78222400	Weak transcription	Fetal Intestine Small	intestine
13	chr1:78197800-78223400	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:78198200-78222200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:78198400-78224000	Weak transcription	Esophagus	oesophagus
16	chr1:78200200-78218800	Weak transcription	HUVEC	blood vessel
17	chr1:78205400-78220200	Weak transcription	GM12878-XiMat	blood
18	chr1:78205400-78221800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:78205600-78222200	Weak transcription	Fetal Brain Male	brain
20	chr1:78206000-78222000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:78206000-78222200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:78206000-78224400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:78206400-78222000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:78206400-78222400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:78206400-78224000	Weak transcription	Fetal Intestine Large	intestine
26	chr1:78206400-78224000	Weak transcription	HSMM	muscle
27	chr1:78206600-78220200	Weak transcription	Dnd41	blood
28	chr1:78206600-78220800	Weak transcription	Hela-S3	cervix
29	chr1:78206600-78221000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:78206600-78221200	Weak transcription	Fetal Thymus	thymus
31	chr1:78206600-78221400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:78206600-78221600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:78206600-78222000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:78206600-78222000	Weak transcription	Primary B cells from cord blood	blood
35	chr1:78206600-78222200	Weak transcription	Brain Germinal Matrix	brain
36	chr1:78206600-78222400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:78206600-78223200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:78206600-78223200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:78206600-78223400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:78206600-78224000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:78206800-78223400	Weak transcription	Fetal Brain Female	brain
42	chr1:78207000-78219800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr1:78207400-78221000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:78207600-78221200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:78208200-78222000	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:78208400-78217800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:78208400-78222000	Weak transcription	Fetal Heart	heart
48	chr1:78208400-78223000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:78210600-78221200	Weak transcription	Left Ventricle	heart
50	chr1:78210600-78221400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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