Variant report

Variant	rs6800475
Chromosome Location	chr3:48492541-48492542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48492410-48492541	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48486792..48490170-chr3:48491410..48494926,8	MCF-7	breast:
2	chr3:48490394..48493256-chr3:48499258..48502604,4	K562	blood:
3	chr3:48486003..48490075-chr3:48490248..48493592,4	K562	blood:
4	chr3:48491396..48492980-chr3:48499258..48501238,2	K562	blood:
5	chr3:48486535..48489941-chr3:48491977..48496128,7	MCF-7	breast:
6	chr3:48485548..48495296-chr3:48503776..48510303,13	MCF-7	breast:
7	chr3:48489543..48493797-chr3:48496122..48499063,3	MCF-7	breast:
8	chr3:48490070..48492746-chr3:48498411..48500259,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000244380	TF binding region
ATRIP	TF binding region
ENSG00000213689	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000244380	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1037773	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10470686	0.95[EUR][1000 genomes]
rs1109227	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130170	0.95[EUR][1000 genomes]
rs11130171	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11712561	0.93[EUR][1000 genomes]
rs11797	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12487542	0.93[EUR][1000 genomes]
rs13069724	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13071337	0.94[EUR][1000 genomes]
rs13072012	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13076076	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13091785	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314659	0.95[EUR][1000 genomes]
rs13324374	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1459242	0.88[EUR][1000 genomes]
rs1459249	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1459250	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1563736	0.94[EUR][1000 genomes]
rs1824363	0.99[ASN][1000 genomes]
rs1870444	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1975844	0.94[EUR][1000 genomes]
rs2045554	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242150	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279077	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290822	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2362450	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2362452	0.88[EUR][1000 genomes]
rs28824259	0.94[EUR][1000 genomes]
rs2885509	0.89[EUR][1000 genomes]
rs2885510	0.89[EUR][1000 genomes]
rs3214041	0.95[EUR][1000 genomes]
rs34761139	0.94[EUR][1000 genomes]
rs35215722	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3774808	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4490383	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858793	0.89[EUR][1000 genomes]
rs4858817	0.89[EUR][1000 genomes]
rs60512868	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442116	0.88[EUR][1000 genomes]
rs6442117	0.91[EUR][1000 genomes]
rs6442118	0.95[EUR][1000 genomes]
rs6442119	0.95[EUR][1000 genomes]
rs6442120	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442123	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442124	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6764415	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6770470	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6776700	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6779262	0.89[EUR][1000 genomes]
rs6784322	0.92[EUR][1000 genomes]
rs6784541	0.92[EUR][1000 genomes]
rs6794875	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6796491	0.94[EUR][1000 genomes]
rs6804774	0.94[EUR][1000 genomes]
rs6810060	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7126	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs725309	0.89[EUR][1000 genomes]
rs725310	0.89[EUR][1000 genomes]
rs73074358	0.93[EUR][1000 genomes]
rs7618883	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7630741	0.90[EUR][1000 genomes]
rs7634377	0.92[EUR][1000 genomes]
rs7635522	0.93[EUR][1000 genomes]
rs7636044	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636782	0.91[EUR][1000 genomes]
rs7639743	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7653691	0.90[EUR][1000 genomes]
rs898225	0.88[EUR][1000 genomes]
rs922075	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311423	0.92[EUR][1000 genomes]
rs9311424	0.92[EUR][1000 genomes]
rs9809843	0.94[EUR][1000 genomes]
rs9812647	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9815103	0.90[EUR][1000 genomes]
rs9817615	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826195	0.94[EUR][1000 genomes]
rs9826247	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838618	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9849509	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862575	0.94[EUR][1000 genomes]
rs9864371	0.94[EUR][1000 genomes]
rs9864815	0.94[EUR][1000 genomes]
rs9875280	0.94[EUR][1000 genomes]
rs9876781	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9876891	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9881491	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9883759	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9883927	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[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	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv876761	chr3:48464968-48496758	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6800475	TMA7	cis	Muscle Skeletal	GTEx
rs6800475	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs6800475	TREX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48489000-48492800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr3:48489000-48492800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:48489000-48492800	Weak transcription	Left Ventricle	heart
4	chr3:48489000-48493200	Weak transcription	Ovary	ovary
5	chr3:48489000-48494400	Weak transcription	Aorta	Aorta
6	chr3:48489200-48492600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:48489200-48492600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:48489200-48492600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:48489200-48492800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:48489200-48493000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:48489200-48494400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:48489200-48494400	Weak transcription	Esophagus	oesophagus
13	chr3:48489200-48494600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:48489200-48494800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:48489200-48498800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:48489200-48506200	Weak transcription	Stomach Mucosa	stomach
17	chr3:48489200-48507400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:48489400-48492600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:48489400-48492600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:48489400-48492600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr3:48489400-48492600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:48489400-48492600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:48489400-48492600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:48489400-48492600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:48489400-48492800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:48489400-48492800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:48489400-48492800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:48489400-48492800	Weak transcription	Brain Anterior Caudate	brain
29	chr3:48489400-48492800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:48489400-48492800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:48489400-48492800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:48489400-48492800	Weak transcription	Fetal Intestine Large	intestine
33	chr3:48489400-48492800	Weak transcription	Fetal Thymus	thymus
34	chr3:48489400-48493200	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:48489400-48493200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:48489400-48493200	Weak transcription	Right Ventricle	heart
37	chr3:48489400-48493200	Weak transcription	HSMM	muscle
38	chr3:48489400-48493400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:48489400-48493800	Weak transcription	Fetal Intestine Small	intestine
40	chr3:48489400-48494400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:48489400-48494400	Weak transcription	Gastric	stomach
42	chr3:48489400-48494400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:48489400-48494400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr3:48489400-48494600	Weak transcription	Brain Angular Gyrus	brain
45	chr3:48489400-48494600	Weak transcription	Brain Substantia Nigra	brain
46	chr3:48489400-48494600	Weak transcription	Fetal Kidney	kidney
47	chr3:48489400-48494600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:48489400-48494600	Weak transcription	HSMMtube	muscle
49	chr3:48489400-48494600	Weak transcription	NHLF	lung
50	chr3:48489400-48494800	Weak transcription	Pancreas	Pancrea

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