Variant report

Variant	rs3173275
Chromosome Location	chr6:33271494-33271495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33271468-33272422	GM12892	blood:	n/a	n/a
2	NFYB	chr6:33271401-33271562	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:33271480-33272308	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:33271224-33274486	K562	blood:	n/a	n/a
5	POLR2A	chr6:33271454-33271877	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:33271433-33274547	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:33271444-33272156	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33259755..33275794-chr6:33276314..33291745,68	MCF-7	breast:
2	chr6:33270764..33273240-chr6:33372859..33374945,2	MCF-7	breast:

Variant related genes	Relation type
RGL2	TF binding region
ENSG00000204209	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000231925	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs57582515	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57745261	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58759132	0.93[AFR][1000 genomes]
rs58883992	0.94[AFR][1000 genomes]
rs59097151	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59142568	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59368071	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59531270	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60170976	0.94[AFR][1000 genomes]
rs60813085	0.84[AFR][1000 genomes]
rs6906693	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6908509	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6920095	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6931141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408048	0.84[AFR][1000 genomes]
rs73408053	0.86[AFR][1000 genomes]
rs73408061	0.92[AFR][1000 genomes]
rs73408065	0.92[AFR][1000 genomes]
rs73408067	0.92[AFR][1000 genomes]
rs73410003	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73410010	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73410043	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73410049	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3173275	TAPBP	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33268000-33271600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr6:33268000-33271600	Weak transcription	Ovary	ovary
3	chr6:33268000-33271800	Weak transcription	Aorta	Aorta
4	chr6:33268000-33272200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:33268000-33272800	Weak transcription	Small Intestine	intestine
6	chr6:33268000-33273600	Weak transcription	Stomach Mucosa	stomach
7	chr6:33268200-33271600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:33268200-33271600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:33268200-33271600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:33268200-33271600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:33268200-33271600	Weak transcription	Brain Substantia Nigra	brain
12	chr6:33268200-33271600	Weak transcription	Colonic Mucosa	Colon
13	chr6:33268200-33271600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:33268200-33271600	Weak transcription	Fetal Kidney	kidney
15	chr6:33268200-33271600	Weak transcription	Gastric	stomach
16	chr6:33268200-33271600	Weak transcription	Lung	lung
17	chr6:33268200-33271600	Weak transcription	Right Ventricle	heart
18	chr6:33268200-33271600	Weak transcription	NHDF-Ad	bronchial
19	chr6:33268200-33271800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:33268200-33272800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:33268200-33273000	Weak transcription	A549	lung
22	chr6:33268200-33279400	Strong transcription	Fetal Intestine Small	intestine
23	chr6:33268200-33279600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:33268200-33279800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:33268200-33279800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:33268200-33279800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:33268200-33279800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr6:33268200-33279800	Weak transcription	Right Atrium	heart
29	chr6:33268200-33279800	Weak transcription	HSMMtube	muscle
30	chr6:33268400-33271600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:33268400-33271600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr6:33268400-33271600	Weak transcription	Esophagus	oesophagus
33	chr6:33268400-33271600	Weak transcription	Pancreas	Pancrea
34	chr6:33268400-33279600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr6:33268400-33279800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:33268600-33273000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:33268600-33279600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:33268600-33279800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:33268600-33279800	Weak transcription	HSMM	muscle
40	chr6:33268800-33271600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr6:33268800-33271600	Weak transcription	HUVEC	blood vessel
42	chr6:33268800-33272000	Weak transcription	Fetal Brain Female	brain
43	chr6:33268800-33279400	Strong transcription	Fetal Thymus	thymus
44	chr6:33268800-33279600	Weak transcription	NH-A	brain
45	chr6:33269000-33271600	Weak transcription	Primary B cells from cord blood	blood
46	chr6:33269000-33273200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:33269000-33274000	Strong transcription	Osteobl	bone
48	chr6:33269000-33274600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr6:33269000-33279800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:33269000-33279800	Weak transcription	Fetal Heart	heart

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