Variant report

Variant	rs55993081
Chromosome Location	chr1:92802759-92802760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:92798322..92801081-chr1:92801191..92803127,2	K562	blood:
2	chr1:92801067..92802871-chr1:92812427..92814790,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122484	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10399671	1.00[EUR][1000 genomes]
rs11164423	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11166542	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070923	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12075168	1.00[EUR][1000 genomes]
rs12075243	1.00[EUR][1000 genomes]
rs12078746	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12090761	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12098095	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17131621	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17131632	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17131636	1.00[EUR][1000 genomes]
rs1819256	0.87[AFR][1000 genomes]
rs41286805	0.87[EUR][1000 genomes]
rs41296171	0.87[EUR][1000 genomes]
rs41313389	0.87[EUR][1000 genomes]
rs4617457	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs56297403	0.87[EUR][1000 genomes]
rs56665661	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57177520	0.87[EUR][1000 genomes]
rs57217458	0.87[EUR][1000 genomes]
rs57992264	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58142139	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59278612	0.87[EUR][1000 genomes]
rs60265386	0.87[EUR][1000 genomes]
rs60550001	0.87[EUR][1000 genomes]
rs60755573	0.87[EUR][1000 genomes]
rs60933677	0.87[EUR][1000 genomes]
rs61141829	0.87[EUR][1000 genomes]
rs61185080	0.87[EUR][1000 genomes]
rs61410146	0.87[EUR][1000 genomes]
rs6603970	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6660858	0.87[EUR][1000 genomes]
rs6661028	0.87[EUR][1000 genomes]
rs6662381	0.93[AFR][1000 genomes]
rs6662565	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6672838	1.00[EUR][1000 genomes]
rs6681027	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6681213	0.87[EUR][1000 genomes]
rs6683456	1.00[EUR][1000 genomes]
rs6694248	0.88[AMR][1000 genomes]
rs6695475	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6702975	0.87[EUR][1000 genomes]
rs6704484	0.87[EUR][1000 genomes]
rs72958740	0.87[EUR][1000 genomes]
rs72958746	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72958774	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72958781	0.87[EUR][1000 genomes]
rs72958796	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72960815	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72960831	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72960835	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72960847	0.87[EUR][1000 genomes]
rs72960860	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72960870	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72960872	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72962640	0.87[EUR][1000 genomes]
rs72962659	1.00[EUR][1000 genomes]
rs74101123	0.87[EUR][1000 genomes]
rs74101131	0.87[EUR][1000 genomes]
rs74101133	0.87[EUR][1000 genomes]
rs74101146	0.87[EUR][1000 genomes]
rs74101152	0.87[EUR][1000 genomes]
rs74101157	0.87[EUR][1000 genomes]
rs74102832	0.87[EUR][1000 genomes]
rs74102844	0.87[EUR][1000 genomes]
rs74102853	0.87[EUR][1000 genomes]
rs74102861	0.87[EUR][1000 genomes]
rs7513631	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7519603	0.87[EUR][1000 genomes]
rs7520555	0.87[EUR][1000 genomes]
rs7520675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7525174	0.87[EUR][1000 genomes]
rs7527960	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7529971	0.87[EUR][1000 genomes]
rs7534750	0.87[EUR][1000 genomes]
rs7535181	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7542362	0.87[EUR][1000 genomes]
rs7546528	0.91[AFR][1000 genomes];0.83[AMR][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	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers 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	33 gene(s)	inside rSNPs	diseases
4	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking 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	14 gene(s)	inside rSNPs	diseases
6	nsv871352	chr1:92761127-92807238	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv870854	chr1:92765102-92807238	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv871387	chr1:92765102-92813741	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92765800-92850000	Weak transcription	Small Intestine	intestine
2	chr1:92771800-92823800	Weak transcription	Colonic Mucosa	Colon
3	chr1:92782200-92803400	Weak transcription	Stomach Mucosa	stomach
4	chr1:92784400-92808200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:92789800-92812000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:92789800-92830600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:92790000-92815200	Weak transcription	Psoas Muscle	Psoas
8	chr1:92790400-92803600	Weak transcription	HUVEC	blood vessel
9	chr1:92792400-92817400	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:92792400-92823600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:92792600-92807600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:92792600-92807800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:92792600-92812400	Weak transcription	Right Ventricle	heart
14	chr1:92792600-92815000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:92792600-92846600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:92792800-92850800	Weak transcription	Fetal Heart	heart
17	chr1:92793600-92817200	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:92793600-92823400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:92793800-92806600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:92793800-92811800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:92793800-92830200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:92794000-92803800	Weak transcription	Brain Anterior Caudate	brain
23	chr1:92794000-92823000	Weak transcription	Brain Substantia Nigra	brain
24	chr1:92794800-92807600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:92795000-92817600	Weak transcription	Brain Germinal Matrix	brain
26	chr1:92795000-92823000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:92795200-92806400	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:92795200-92806600	Weak transcription	Fetal Stomach	stomach
29	chr1:92795200-92807200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:92795200-92815200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:92795200-92817000	Weak transcription	Esophagus	oesophagus
32	chr1:92795200-92817000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:92795200-92823400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:92795200-92825000	Weak transcription	Aorta	Aorta
35	chr1:92795200-92825000	Weak transcription	Lung	lung
36	chr1:92795200-92830400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:92795200-92846600	Weak transcription	Gastric	stomach
38	chr1:92795200-92850200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:92795200-92851400	Weak transcription	Spleen	Spleen
40	chr1:92795400-92807000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:92795400-92825200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:92795600-92803800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:92795600-92814400	Weak transcription	A549	lung
44	chr1:92795600-92825200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:92795600-92826400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:92795600-92831200	Weak transcription	NHLF	lung
47	chr1:92795800-92803600	Weak transcription	Fetal Kidney	kidney
48	chr1:92795800-92803800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:92795800-92803800	Weak transcription	Primary T cells from cord blood	blood
50	chr1:92795800-92803800	Weak transcription	Left Ventricle	heart

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