Variant report

Variant	rs278847
Chromosome Location	chr1:78153821-78153822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78153418..78155756-chr1:78236442..78239366,2	K562	blood:
2	chr1:78148636..78150222-chr1:78153007..78155635,3	MCF-7	breast:
3	chr1:78147916..78149547-chr1:78151862..78154484,2	MCF-7	breast:
4	chr1:78153612..78156248-chr1:78205840..78207802,2	K562	blood:

Variant related genes	Relation type
ENSG00000036549	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1038983	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10873951	0.93[ASN][1000 genomes]
rs11162364	0.81[ASN][1000 genomes]
rs11162365	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11162366	0.82[EUR][1000 genomes]
rs11162369	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162372	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162380	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11162383	0.80[AMR][1000 genomes]
rs11162387	0.80[AMR][1000 genomes]
rs11578805	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1166584	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12026939	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12128041	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12142671	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12717767	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1565850	0.81[ASN][1000 genomes]
rs1565851	0.81[ASN][1000 genomes]
rs1565852	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1962523	0.85[ASN][1000 genomes]
rs1977900	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2147318	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2172727	0.81[ASN][1000 genomes]
rs2274123	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs278833	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278836	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278838	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278843	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278845	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs278852	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278854	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs278857	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278858	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278859	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278862	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278864	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3509	0.83[ASN][1000 genomes]
rs366467	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs370335	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs371076	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4245658	0.81[ASN][1000 genomes]
rs4949661	0.84[EUR][1000 genomes]
rs4949809	0.81[ASN][1000 genomes]
rs4949811	0.81[ASN][1000 genomes]
rs4949813	0.85[ASN][1000 genomes]
rs4949814	0.82[EUR][1000 genomes]
rs4949816	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4949822	0.84[AMR][1000 genomes]
rs5025902	0.83[EUR][1000 genomes]
rs56688304	0.82[EUR][1000 genomes]
rs6603955	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6603956	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6657290	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6667519	0.81[ASN][1000 genomes]
rs6670660	0.84[EUR][1000 genomes]
rs6672200	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6674638	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6675743	0.81[ASN][1000 genomes]
rs6687596	0.82[EUR][1000 genomes]
rs6691317	0.83[EUR][1000 genomes]
rs6693100	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6698151	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs728741	0.85[ASN][1000 genomes]
rs7513619	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7521042	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7524866	0.81[ASN][1000 genomes]
rs7545175	0.84[EUR][1000 genomes]
rs7552291	0.81[EUR][1000 genomes]
rs962388	0.85[ASN][1000 genomes]
rs9662527	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
5	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
6	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
7	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
8	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
9	nsv946004	chr1:78152199-78160377	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv3348629	chr1:78152214-78154612	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs278847	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78149600-78175000	Weak transcription	Gastric	stomach
2	chr1:78149600-78177800	Weak transcription	Spleen	Spleen
3	chr1:78149800-78157400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:78149800-78157600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:78149800-78158800	Weak transcription	Left Ventricle	heart
6	chr1:78149800-78159800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:78149800-78165600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:78149800-78165600	Weak transcription	Esophagus	oesophagus
9	chr1:78149800-78165600	Weak transcription	Lung	lung
10	chr1:78149800-78171800	Weak transcription	Fetal Brain Male	brain
11	chr1:78149800-78173000	Weak transcription	Colonic Mucosa	Colon
12	chr1:78149800-78173800	Weak transcription	Aorta	Aorta
13	chr1:78149800-78178000	Weak transcription	Small Intestine	intestine
14	chr1:78150000-78158600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:78150000-78158800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:78150000-78158800	Weak transcription	Fetal Brain Female	brain
17	chr1:78150000-78160800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:78150000-78160800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:78150000-78161600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:78150000-78162000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:78150000-78163000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:78150000-78165200	Weak transcription	Brain Angular Gyrus	brain
23	chr1:78150000-78166000	Weak transcription	HSMMtube	muscle
24	chr1:78150000-78172800	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:78150000-78173000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:78150000-78173000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:78150000-78173600	Weak transcription	Psoas Muscle	Psoas
28	chr1:78150000-78174000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:78150000-78175600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:78150200-78154600	Weak transcription	GM12878-XiMat	blood
31	chr1:78150200-78155000	Weak transcription	Primary T cells from cord blood	blood
32	chr1:78150200-78157400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:78150200-78157600	Weak transcription	Osteobl	bone
34	chr1:78150200-78158000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:78150200-78158000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:78150200-78158800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:78150200-78158800	Weak transcription	HSMM	muscle
38	chr1:78150200-78159800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:78150200-78160800	Weak transcription	Brain Germinal Matrix	brain
40	chr1:78150200-78160800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:78150200-78161000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:78150200-78170400	Weak transcription	HUVEC	blood vessel
43	chr1:78150200-78172600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:78150200-78173400	Weak transcription	HMEC	breast
45	chr1:78150200-78175600	Weak transcription	Brain Substantia Nigra	brain
46	chr1:78150400-78154800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:78150400-78154800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:78150400-78157200	Weak transcription	Primary B cells from cord blood	blood
49	chr1:78150400-78157600	Weak transcription	Fetal Lung	lung
50	chr1:78150400-78159800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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