Variant report

Variant	rs56753982
Chromosome Location	chr5:177649675-177649676
allele	C/T
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	chr5:177647680-177651473	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:177649468-177650387	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:177647997-177651461	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr5:177649210-177650948	GM12892	blood:	n/a	n/a
5	POLR2A	chr5:177649567-177649677	A549	lung:	n/a	n/a
6	POLR2A	chr5:177647806-177652259	GM12891	blood:	n/a	n/a
7	POLR2A	chr5:177649200-177650466	K562	blood:	n/a	n/a
8	POLR2A	chr5:177647467-177652584	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:177648283-177651899	K562	blood:	n/a	n/a
10	POLR2A	chr5:177649282-177650347	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:177649663-177649851	HUVEC	blood vessel:	n/a	n/a
12	STAT3	chr5:177649553-177649753	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr5:177647972-177652526	GM12878	blood:	n/a	n/a
14	POLR2A	chr5:177647479-177653078	K562	blood:	n/a	n/a
15	POLR2A	chr5:177648258-177651864	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:177648029-177652545	GM12878	blood:	n/a	n/a
17	POLR2A	chr5:177649458-177649791	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr5:177649048-177651522	HEK293	kidney:	n/a	n/a
19	POLR2A	chr5:177647582-177650509	IMR90	lung:	n/a	n/a
20	POLR2A	chr5:177647876-177651962	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr5:177647699-177653070	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr5:177647352-177652340	GM12892	blood:	n/a	n/a
23	POLR2A	chr5:177648800-177650639	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr5:177647865-177650606	GM12892	blood:	n/a	n/a
25	POLR2A	chr5:177649168-177649719	GM12891	blood:	n/a	n/a
26	POLR2A	chr5:177648141-177652962	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr5:177649222-177651910	GM18505	blood:	n/a	n/a
28	POLR2A	chr5:177648073-177652554	HL-60	blood:	n/a	n/a
29	POLR2A	chr5:177649555-177652009	K562	blood:	n/a	n/a
30	POLR2A	chr5:177649495-177650093	HepG2	liver:	n/a	n/a
31	JUND	chr5:177649524-177650618	A549	lung:	n/a	chr5:177650085-177650093
32	POLR2A	chr5:177647476-177652787	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr5:177649234-177650702	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr5:177645181-177652644	A549	lung:	n/a	n/a
35	POLR2A	chr5:177649491-177651678	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr5:177647525-177652315	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
PHYKPL	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs57594195	1.00[AMR][1000 genomes]
rs61473059	1.00[AMR][1000 genomes]
rs6881230	1.00[AMR][1000 genomes]
rs73336845	1.00[AMR][1000 genomes]
rs73336889	1.00[AMR][1000 genomes]
rs73338871	1.00[AMR][1000 genomes]
rs73342844	1.00[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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	106 gene(s)	inside rSNPs	diseases
5	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
6	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
7	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 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	chr5:177634000-177650800	Strong transcription	Placenta	Placenta
2	chr5:177634400-177654200	Strong transcription	Fetal Stomach	stomach
3	chr5:177635000-177650200	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:177635000-177650400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:177635000-177650400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:177635000-177650400	Strong transcription	Adipose Nuclei	Adipose
7	chr5:177635400-177651000	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr5:177635800-177657000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr5:177636000-177654000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:177639400-177657600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:177640000-177650400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:177640400-177655600	Weak transcription	Right Atrium	heart
13	chr5:177641000-177650800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:177642600-177654200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:177643200-177651000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr5:177643400-177650200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:177643400-177650600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:177643400-177651600	Weak transcription	HSMMtube	muscle
19	chr5:177643400-177656400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:177643600-177650400	Weak transcription	Fetal Heart	heart
21	chr5:177643600-177654400	Weak transcription	Aorta	Aorta
22	chr5:177643600-177655200	Weak transcription	Stomach Mucosa	stomach
23	chr5:177643800-177650200	Weak transcription	HMEC	breast
24	chr5:177643800-177652200	Strong transcription	Liver	Liver
25	chr5:177643800-177653800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:177644000-177650000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:177644000-177651400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:177644200-177654800	Weak transcription	NHDF-Ad	bronchial
29	chr5:177645400-177650200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:177645400-177651400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr5:177645400-177651600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr5:177645400-177654800	Strong transcription	Hela-S3	cervix
33	chr5:177645400-177656800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr5:177645400-177656800	Strong transcription	Dnd41	blood
35	chr5:177645600-177654800	Weak transcription	HSMM	muscle
36	chr5:177645800-177650000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:177646000-177651400	Weak transcription	NH-A	brain
38	chr5:177646000-177654400	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:177646200-177654000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:177646200-177657000	Weak transcription	Fetal Brain Male	brain
41	chr5:177646400-177652000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:177646600-177653000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:177646600-177657400	Strong transcription	Thymus	Thymus
44	chr5:177646800-177654400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:177646800-177658000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:177647400-177652400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr5:177647600-177650400	Strong transcription	Osteobl	bone
48	chr5:177647600-177653200	Strong transcription	A549	lung
49	chr5:177647600-177654400	Genic enhancers	Fetal Intestine Small	intestine
50	chr5:177647800-177649800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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