Variant report

Variant	rs28425483
Chromosome Location	chr5:176977611-176977612
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:176977467-176977890	K562	blood:	n/a	n/a
2	POLR2A	chr5:176977336-176977677	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:176977356-176977671	HUVEC	blood vessel:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:176976066..176978459-chr5:177019128..177020670,2	K562	blood:
2	chr5:176975793..176978264-chr5:177036899..177039558,2	K562	blood:
3	chr5:176950247..176952625-chr5:176975768..176978553,2	K562	blood:
4	chr5:176977384..176979109-chr5:177015440..177017120,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMED9-3	chr5:176973789-176978411	l_3071_chr5:176970058-176981391_testes

No data

Variant related genes	Relation type
ENSG00000272459	TF binding region
ENSG00000146067	Chromatin interaction
ENSG00000247679	Chromatin interaction
ENSG00000184840	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2544814	0.90[JPT][hapmap]

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	nsv883164	chr5:176780545-177003616	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv883177	chr5:176868358-177003616	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	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
6	nsv5147	chr5:176938196-176983018	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	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
8	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:176947000-176979000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr5:176950000-176978600	Strong transcription	Dnd41	blood
3	chr5:176960000-176979400	Weak transcription	Stomach Mucosa	stomach
4	chr5:176962400-176980000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:176964200-176980000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:176966200-176978400	Weak transcription	Spleen	Spleen
7	chr5:176966200-176979400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr5:176966200-176979800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr5:176966200-176980000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:176966600-176978000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:176966800-176980200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:176967000-176979600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:176968200-176979200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:176969600-176979800	Weak transcription	Fetal Kidney	kidney
15	chr5:176970000-176978800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:176972800-176979200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr5:176973200-176978400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:176973200-176979200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:176973200-176980000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:176974000-176977800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr5:176974000-176978200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr5:176974000-176979600	Weak transcription	Lung	lung
23	chr5:176974000-176979600	Weak transcription	Ovary	ovary
24	chr5:176974000-176980000	Weak transcription	Colonic Mucosa	Colon
25	chr5:176974000-176980000	Weak transcription	Gastric	stomach
26	chr5:176974000-176980200	Weak transcription	Aorta	Aorta
27	chr5:176974000-176980400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr5:176974200-176978400	Weak transcription	Primary B cells from cord blood	blood
29	chr5:176974200-176979600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:176974200-176979600	Strong transcription	Fetal Stomach	stomach
31	chr5:176974800-176979600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr5:176974800-176980000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr5:176975000-176978000	Weak transcription	Hela-S3	cervix
34	chr5:176975000-176979000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:176975000-176979600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:176975000-176979600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:176975000-176979600	Strong transcription	Fetal Muscle Trunk	muscle
38	chr5:176975200-176979000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr5:176975200-176979800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:176975200-176980000	Weak transcription	Brain Substantia Nigra	brain
41	chr5:176975400-176978600	Weak transcription	Fetal Brain Female	brain
42	chr5:176975400-176979200	Weak transcription	A549	lung
43	chr5:176975600-176979200	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:176975800-176978400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr5:176975800-176978600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:176975800-176979000	Weak transcription	Brain Anterior Caudate	brain
47	chr5:176975800-176979200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:176975800-176979400	Weak transcription	Fetal Brain Male	brain
49	chr5:176975800-176979600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr5:176975800-176979600	Weak transcription	Small Intestine	intestine

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