Variant report

Variant	rs6693100
Chromosome Location	chr1:78175022-78175023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78170863..78172598-chr1:78174787..78177234,2	K562	blood:
2	chr1:78168122..78170509-chr1:78172937..78175647,4	K562	blood:
3	chr1:78147992..78150631-chr1:78173939..78175492,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000036549	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1038983	0.81[EUR][1000 genomes]
rs10873951	0.85[ASN][1000 genomes]
rs11162365	0.87[EUR][1000 genomes]
rs11162369	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11162372	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11162380	0.83[EUR][1000 genomes]
rs11578805	0.84[EUR][1000 genomes]
rs1166584	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1166585	0.82[EUR][1000 genomes]
rs1166586	0.82[AMR][1000 genomes]
rs1166588	0.83[EUR][1000 genomes]
rs12026939	0.81[EUR][1000 genomes]
rs12128041	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12142671	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12717767	0.87[EUR][1000 genomes]
rs1565852	0.88[EUR][1000 genomes]
rs1977900	0.82[EUR][1000 genomes]
rs2147318	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2274123	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs278833	0.84[EUR][1000 genomes]
rs278836	0.81[EUR][1000 genomes]
rs278838	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs278843	0.84[EUR][1000 genomes]
rs278845	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278847	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278852	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278854	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278857	0.83[EUR][1000 genomes]
rs278858	0.83[EUR][1000 genomes]
rs278859	0.84[EUR][1000 genomes]
rs278862	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs278864	0.84[EUR][1000 genomes]
rs366467	0.81[EUR][1000 genomes]
rs370335	0.81[EUR][1000 genomes]
rs371076	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4949816	0.87[EUR][1000 genomes]
rs5025902	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56688304	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6603955	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6603956	0.81[EUR][1000 genomes]
rs6657290	0.81[EUR][1000 genomes]
rs6672200	0.81[EUR][1000 genomes]
rs6674638	0.80[EUR][1000 genomes]
rs6687596	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6698151	0.80[EUR][1000 genomes]
rs7513619	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7521042	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9662527	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	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
7	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
8	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
rs6693100	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78149600-78177800	Weak transcription	Spleen	Spleen
2	chr1:78149800-78178000	Weak transcription	Small Intestine	intestine
3	chr1:78150000-78175600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:78150200-78175600	Weak transcription	Brain Substantia Nigra	brain
5	chr1:78153400-78175600	Weak transcription	HepG2	liver
6	chr1:78153800-78175400	Weak transcription	NHEK	skin
7	chr1:78153800-78177000	Weak transcription	Right Ventricle	heart
8	chr1:78153800-78178000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:78155800-78178000	Weak transcription	Pancreas	Pancrea
10	chr1:78161000-78187400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:78161600-78178000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:78165800-78178000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:78166200-78175400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:78166200-78175600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:78167600-78176800	Weak transcription	Fetal Intestine Small	intestine
16	chr1:78168600-78186000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:78171200-78184200	Strong transcription	Primary B cells from cord blood	blood
18	chr1:78171400-78176800	Strong transcription	HSMM	muscle
19	chr1:78171400-78182400	Strong transcription	Primary hematopoietic stem cells	blood
20	chr1:78171400-78184600	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr1:78171400-78206600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:78171600-78199000	Strong transcription	Adipose Nuclei	Adipose
23	chr1:78171600-78207400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:78171800-78177600	Strong transcription	Fetal Brain Male	brain
25	chr1:78171800-78178200	Strong transcription	GM12878-XiMat	blood
26	chr1:78171800-78178600	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr1:78171800-78184600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:78171800-78197600	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:78171800-78198000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:78171800-78200200	Strong transcription	Fetal Lung	lung
31	chr1:78171800-78205600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:78171800-78206800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr1:78171800-78206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:78171800-78206800	Strong transcription	Placenta	Placenta
35	chr1:78171800-78207000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr1:78171800-78207200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:78172000-78182400	Strong transcription	Stomach Smooth Muscle	stomach
38	chr1:78172000-78197800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:78172000-78198800	Strong transcription	Primary T cells from cord blood	blood
40	chr1:78172000-78206000	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr1:78172200-78176200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:78172200-78176600	Strong transcription	Brain Angular Gyrus	brain
43	chr1:78172200-78176600	Strong transcription	HSMMtube	muscle
44	chr1:78172200-78179400	Strong transcription	Ovary	ovary
45	chr1:78172200-78180200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:78172200-78183600	Strong transcription	Liver	Liver
47	chr1:78172200-78184200	Strong transcription	Primary B cells from peripheral blood	blood
48	chr1:78172200-78184400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:78172200-78188200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr1:78172200-78195800	Strong transcription	Fetal Thymus	thymus

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