Variant report

Variant	rs55907643
Chromosome Location	chr16:75659812-75659813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75658658-75661263	GM12878	blood:	n/a	n/a
2	POLR2A	chr16:75659424-75660284	HL-60	blood:	n/a	n/a
3	POLR2A	chr16:75659345-75660411	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr16:75659288-75660140	K562	blood:	n/a	n/a
5	POLR2A	chr16:75659371-75660459	U87	brain:	n/a	n/a
6	POLR2A	chr16:75659416-75659871	HCT-116	colon:	n/a	n/a
7	POLR2A	chr16:75659575-75661350	HepG2	liver:	n/a	n/a
8	POLR2A	chr16:75659464-75660333	K562	blood:	n/a	n/a
9	POLR2A	chr16:75658339-75662100	K562	blood:	n/a	n/a
10	POLR2A	chr16:75659149-75659972	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr16:75659695-75660653	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr16:75659512-75661313	GM12878	blood:	n/a	n/a
13	POLR2A	chr16:75659396-75661359	GM12891	blood:	n/a	n/a
14	POLR2A	chr16:75659755-75660296	GM12891	blood:	n/a	n/a
15	POLR2A	chr16:75659597-75660258	GM12878	blood:	n/a	n/a
16	POLR2A	chr16:75659479-75659836	HepG2	liver:	n/a	n/a
17	POLR2A	chr16:75659413-75660194	GM12892	blood:	n/a	n/a
18	POLR2A	chr16:75659485-75661464	GM12892	blood:	n/a	n/a
19	POLR2A	chr16:75659377-75660459	U87	brain:	n/a	n/a
20	POLR2A	chr16:75659264-75660320	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr16:75659632-75659942	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr16:75658427-75661240	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr16:75659356-75661414	GM12878	blood:	n/a	n/a
24	POLR2A	chr16:75658750-75661468	GM12892	blood:	n/a	n/a
25	POLR2A	chr16:75659434-75660086	HL-60	blood:	n/a	n/a
26	POLR2A	chr16:75659394-75660337	K562	blood:	n/a	n/a
27	POLR2A	chr16:75659354-75661366	GM12892	blood:	n/a	n/a
28	POLR2A	chr16:75659389-75660283	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr16:75659404-75660129	GM12891	blood:	n/a	n/a
30	POLR2A	chr16:75659353-75661250	K562	blood:	n/a	n/a
31	POLR2A	chr16:75659324-75660223	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr16:75658438-75661358	K562	blood:	n/a	n/a
33	POLR2A	chr16:75659545-75661204	A549	lung:	n/a	n/a
34	POLR2A	chr16:75658309-75660431	GM12891	blood:	n/a	n/a
35	POLR2A	chr16:75659455-75660383	GM12891	blood:	n/a	n/a
36	POLR2A	chr16:75658173-75661283	HepG2	liver:	n/a	n/a
37	POLR2A	chr16:75659405-75660492	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:75653410..75664044-chr16:75674901..75683254,27	MCF-7	breast:
2	chr16:75656276..75657906-chr16:75659788..75662087,2	K562	blood:
3	chr16:75659014..75660768-chr16:75697180..75699585,2	K562	blood:
4	chr16:75589260..75591107-chr16:75659674..75662120,3	K562	blood:
5	chr16:75657575..75660542-chr16:75680530..75682857,2	K562	blood:

No data

Variant related genes	Relation type
ADAT1	TF binding region
ENSG00000065427	Chromatin interaction
ENSG00000166848	Chromatin interaction
ENSG00000205084	Chromatin interaction
ENSG00000065457	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs56029288	0.84[AFR][1000 genomes]
rs56146953	1.00[AMR][1000 genomes]
rs56235797	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58718680	1.00[AMR][1000 genomes]
rs59487462	0.86[AFR][1000 genomes]
rs59619831	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59634477	1.00[AMR][1000 genomes]
rs60545964	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60713528	0.93[AFR][1000 genomes]
rs60768865	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61675014	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7191923	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7192136	1.00[AMR][1000 genomes]
rs73613298	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73615046	0.82[AFR][1000 genomes]
rs73615053	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73615054	0.82[AFR][1000 genomes]
rs73615069	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73615080	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73615207	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73615239	1.00[AMR][1000 genomes]
rs73615244	1.00[AMR][1000 genomes]
rs73615275	1.00[AMR][1000 genomes]
rs8047796	0.84[AFR][1000 genomes]
rs8058139	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1062010	chr16:75628562-75825725	Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1064880	chr16:75628562-75895699	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv542960	chr16:75628562-75895699	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1065543	chr16:75631306-75800170	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 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	chr16:75656800-75667800	Weak transcription	Fetal Heart	heart
2	chr16:75657200-75660000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr16:75657200-75660200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:75657400-75661600	Weak transcription	Small Intestine	intestine
5	chr16:75657600-75660000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr16:75657600-75660200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr16:75657600-75660200	Weak transcription	Aorta	Aorta
8	chr16:75657600-75660200	Weak transcription	Pancreas	Pancrea
9	chr16:75657600-75660200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr16:75657600-75661800	Weak transcription	Colonic Mucosa	Colon
11	chr16:75657600-75666200	Weak transcription	Fetal Brain Male	brain
12	chr16:75657600-75668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr16:75657800-75660000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr16:75657800-75660000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr16:75657800-75660000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr16:75657800-75660000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr16:75657800-75660000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr16:75657800-75660000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr16:75657800-75660000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr16:75657800-75660000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr16:75657800-75660000	Weak transcription	NH-A	brain
22	chr16:75657800-75660200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr16:75657800-75660800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr16:75657800-75661000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr16:75657800-75661000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr16:75657800-75661000	Weak transcription	Colon Smooth Muscle	Colon
27	chr16:75657800-75661800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr16:75657800-75661800	Weak transcription	NHDF-Ad	bronchial
29	chr16:75658000-75660000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr16:75658000-75660000	Weak transcription	Fetal Intestine Small	intestine
31	chr16:75658000-75660200	Weak transcription	Esophagus	oesophagus
32	chr16:75658400-75660600	Strong transcription	Fetal Thymus	thymus
33	chr16:75658400-75679200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr16:75658400-75679800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr16:75658400-75679800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr16:75658600-75660400	Genic enhancers	K562	blood
37	chr16:75658600-75660600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr16:75658600-75678200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr16:75658800-75660400	Strong transcription	Primary T cells from cord blood	blood
40	chr16:75658800-75661000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr16:75658800-75672400	Strong transcription	Fetal Brain Female	brain
42	chr16:75658800-75672600	Strong transcription	GM12878-XiMat	blood
43	chr16:75658800-75677000	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr16:75658800-75679800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr16:75659000-75660800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr16:75659000-75662000	Strong transcription	Primary B cells from cord blood	blood
47	chr16:75659000-75662000	Strong transcription	Dnd41	blood
48	chr16:75659000-75671800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr16:75659000-75672000	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr16:75659000-75677000	Strong transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links