Variant report

Variant	rs1843633
Chromosome Location	chr5:177024338-177024339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:177022632-177024414	K562	blood:	n/a	n/a
2	POLR2A	chr5:177020438-177025170	K562	blood:	n/a	n/a
3	POLR2A	chr5:177023326-177024405	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:177021812-177024422	GM12892	blood:	n/a	n/a
5	POLR2A	chr5:177021724-177024535	GM12878	blood:	n/a	n/a
6	POLR2A	chr5:177021795-177024456	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:176992384..176993998-chr5:177022547..177024754,2	K562	blood:
2	chr5:176994913..176997833-chr5:177022408..177024826,2	K562	blood:
3	chr5:176978409..176982516-chr5:177021399..177024969,5	MCF-7	breast:
4	chr5:176895756..176898053-chr5:177023963..177026358,2	K562	blood:
5	chr5:177010880..177013120-chr5:177024317..177026904,2	K562	blood:

No data

Variant related genes	Relation type
B4GALT7	TF binding region
ENSG00000272459	Chromatin interaction
ENSG00000146067	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11490750	0.81[ASN][1000 genomes]
rs168080	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs168081	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs186803	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1872624	0.81[ASN][1000 genomes]
rs2046511	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs234375	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28375402	0.81[ASN][1000 genomes]
rs28403900	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28461466	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28496282	0.84[ASN][1000 genomes]
rs28757437	0.81[ASN][1000 genomes]
rs337340	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs337361	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs337364	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337365	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs430797	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs446709	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6600950	0.83[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	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
3	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv1022630	chr5:176975746-177028082	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv537966	chr5:176975746-177028082	Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv883181	chr5:176978496-177034786	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv883183	chr5:177019379-177030351	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1843633	TMED9	Cis_1M	lymphoblastoid	RTeQTL
rs1843633	B4GALT7	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177021000-177024400	Strong transcription	Fetal Stomach	stomach
2	chr5:177021400-177026200	Weak transcription	Fetal Heart	heart
3	chr5:177021600-177026800	Weak transcription	Fetal Brain Male	brain
4	chr5:177022200-177025600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:177022400-177026200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:177022400-177026200	Weak transcription	Fetal Kidney	kidney
7	chr5:177023000-177024400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:177023000-177025600	Weak transcription	Stomach Mucosa	stomach
9	chr5:177023000-177026000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:177023200-177026200	Weak transcription	Psoas Muscle	Psoas
11	chr5:177023400-177025600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr5:177023400-177025600	Weak transcription	Hela-S3	cervix
13	chr5:177023400-177026200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:177023400-177026200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:177023400-177026200	Weak transcription	Colon Smooth Muscle	Colon
16	chr5:177023600-177024600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:177023600-177025600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:177023600-177025600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr5:177023600-177026200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:177023600-177026200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:177023800-177025200	Weak transcription	K562	blood
22	chr5:177023800-177025400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr5:177023800-177025400	Weak transcription	HepG2	liver
24	chr5:177023800-177025400	Weak transcription	Osteobl	bone
25	chr5:177023800-177025600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:177023800-177025600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr5:177023800-177025600	Weak transcription	Primary B cells from cord blood	blood
28	chr5:177023800-177025600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr5:177023800-177025600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr5:177023800-177025600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:177023800-177026000	Weak transcription	Brain Anterior Caudate	brain
32	chr5:177023800-177026200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr5:177023800-177026200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:177023800-177026200	Weak transcription	Brain Angular Gyrus	brain
35	chr5:177023800-177026200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr5:177023800-177026200	Weak transcription	Brain Substantia Nigra	brain
37	chr5:177023800-177026200	Weak transcription	Pancreas	Pancrea
38	chr5:177023800-177026200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:177023800-177026200	Weak transcription	NHDF-Ad	bronchial
40	chr5:177023800-177026600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:177023800-177026600	Weak transcription	Aorta	Aorta
42	chr5:177023800-177026600	Weak transcription	Gastric	stomach
43	chr5:177023800-177026600	Weak transcription	HSMM	muscle
44	chr5:177023800-177026600	Weak transcription	HSMMtube	muscle
45	chr5:177024000-177024800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr5:177024000-177024800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr5:177024000-177025000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr5:177024000-177025000	Weak transcription	HUVEC	blood vessel
49	chr5:177024000-177025400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr5:177024000-177025400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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