Variant report

Variant	rs72898320
Chromosome Location	chr1:45973628-45973629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:84)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:84 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr1:45973568-45975082	GM12878	blood:	n/a	n/a
2	JUND	chr1:45972871-45975112	A549	lung:	n/a	chr1:45973476-45973490
3	POLR2A	chr1:45972866-45975153	HCT-116	colon:	n/a	n/a
4	POLR2A	chr1:45973385-45974853	U87	brain:	n/a	n/a
5	POLR2A	chr1:45973000-45974988	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:45972808-45975056	H1-hESC	embryonic stem cell:	n/a	n/a
7	RXRA	chr1:45973607-45973942	HepG2	liver:	n/a	n/a
8	MAFK	chr1:45973556-45973666	Hela-S3	cervix:	n/a	n/a
9	FOXA1	chr1:45973548-45974343	HepG2	liver:	n/a	n/a
10	SIX5	chr1:45973129-45974123	A549	lung:	n/a	chr1:45973328-45973344 chr1:45973328-45973344 chr1:45973328-45973344 chr1:45973328-45973344 chr1:45973328-45973344 chr1:45973328-45973344
11	POLR2A	chr1:45972877-45974916	A549	lung:	n/a	n/a
12	REST	chr1:45973431-45974663	A549	lung:	n/a	n/a
13	POLR2A	chr1:45972838-45975218	PANC-1	pancreas:	n/a	n/a
14	JUND	chr1:45972476-45975008	A549	lung:	n/a	chr1:45973476-45973490
15	POLR2A	chr1:45973274-45974958	U87	brain:	n/a	n/a
16	POLR2A	chr1:45972867-45979125	Hela-S3	cervix:	n/a	n/a
17	BHLHE40	chr1:45973412-45973795	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:45972932-45976748	GM12892	blood:	n/a	n/a
19	ZBTB33	chr1:45973418-45974227	A549	lung:	n/a	n/a
20	ELF1	chr1:45972954-45974760	A549	lung:	n/a	n/a
21	POLR2A	chr1:45972796-45975088	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:45973197-45975216	GM12891	blood:	n/a	n/a
23	POLR2A	chr1:45972821-45975013	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:45973208-45975384	K562	blood:	n/a	n/a
25	POLR2A	chr1:45973399-45974958	U87	brain:	n/a	n/a
26	POLR2A	chr1:45972667-45975035	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr1:45972687-45978691	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr1:45972840-45975205	K562	blood:	n/a	n/a
29	POLR2A	chr1:45973577-45974973	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:45973017-45975225	GM12892	blood:	n/a	n/a
31	ATF3	chr1:45973345-45974842	A549	lung:	n/a	n/a
32	POLR2A	chr1:45973292-45977716	HepG2	liver:	n/a	n/a
33	TCF12	chr1:45972856-45974890	A549	lung:	n/a	chr1:45973677-45973684
34	FOXA2	chr1:45973582-45974272	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:45972974-45979094	K562	blood:	n/a	n/a
36	POLR2A	chr1:45973506-45975087	HCT-116	colon:	n/a	n/a
37	PBX3	chr1:45973017-45974188	A549	lung:	n/a	n/a
38	POLR2A	chr1:45972877-45977732	HepG2	liver:	n/a	n/a
39	MAX	chr1:45973388-45974403	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:45972966-45975090	HepG2	liver:	n/a	n/a
41	REST	chr1:45973280-45973795	A549	lung:	n/a	n/a
42	MAX	chr1:45973585-45973748	HepG2	liver:	n/a	n/a
43	POLR2A	chr1:45973185-45976753	PANC-1	pancreas:	n/a	n/a
44	MAX	chr1:45973246-45974529	A549	lung:	n/a	n/a
45	POLR2A	chr1:45973509-45973736	HUVEC	blood vessel:	n/a	n/a
46	SIN3AK20	chr1:45972815-45974599	A549	lung:	n/a	n/a
47	BCL3	chr1:45972281-45975128	A549	lung:	n/a	chr1:45972464-45972473
48	POLR2A	chr1:45973256-45975023	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr1:45973135-45974962	HUVEC	blood vessel:	n/a	n/a
50	FOXA1	chr1:45973514-45974285	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45972529..45974569-chr1:46033320..46036119,2	MCF-7	breast:
2	chr1:45972767..45974304-chr1:46039504..46041198,2	K562	blood:
3	chr1:45973068..45975148-chr1:46049390..46051110,2	MCF-7	breast:
4	chr1:45973182..45975128-chr1:45984664..45989019,3	MCF-7	breast:
5	chr1:45965671..45969478-chr1:45972057..45975317,5	MCF-7	breast:
6	chr1:45811184..45813641-chr1:45972187..45974707,2	K562	blood:
7	chr1:45972145..45974948-chr1:46590172..46592785,2	K562	blood:
8	chr1:45805983..45807549-chr1:45973532..45975768,2	K562	blood:
9	chr1:45972293..45974739-chr1:46350771..46352345,2	K562	blood:

No data

Variant related genes	Relation type
MMACHC	TF binding region
ENSG00000132763	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000236624	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11211125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211127	1.00[EUR][1000 genomes]
rs12065695	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12067882	1.00[EUR][1000 genomes]
rs12070890	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12073047	1.00[EUR][1000 genomes]
rs12083690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12091335	1.00[EUR][1000 genomes]
rs12093444	1.00[EUR][1000 genomes]
rs12565230	1.00[EUR][1000 genomes]
rs16832540	1.00[EUR][1000 genomes]
rs16832545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16832550	1.00[EUR][1000 genomes]
rs16832557	1.00[EUR][1000 genomes]
rs16832559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1855621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28532613	1.00[EUR][1000 genomes]
rs28674795	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2934860	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2934861	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2934863	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2934864	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2991965	0.92[AFR][1000 genomes]
rs2991967	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2991969	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2991984	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2993256	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2993260	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2993261	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3014222	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3014223	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3014224	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3014226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35067820	1.00[EUR][1000 genomes]
rs35103566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36053912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57910611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59050426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60347972	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60660559	1.00[EUR][1000 genomes]
rs6664588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6671347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6677135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6699702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72896187	1.00[EUR][1000 genomes]
rs72898313	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898323	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7412911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7536559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7550744	1.00[EUR][1000 genomes]
rs9429080	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9429083	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9429164	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9429165	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription 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 miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
2	chr1:45966400-45975600	Weak transcription	HSMMtube	muscle
3	chr1:45966400-45975800	Weak transcription	Aorta	Aorta
4	chr1:45966600-45984600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:45966800-45973800	Weak transcription	Brain Germinal Matrix	brain
6	chr1:45966800-45974200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:45966800-45975800	Weak transcription	HSMM	muscle
8	chr1:45966800-45975800	Weak transcription	NHDF-Ad	bronchial
9	chr1:45966800-45976000	Weak transcription	Fetal Brain Male	brain
10	chr1:45966800-45976000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:45966800-45980200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:45966800-45984800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:45967000-45973800	Weak transcription	Ovary	ovary
14	chr1:45967000-45974000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:45967000-45974000	Weak transcription	Colonic Mucosa	Colon
16	chr1:45967000-45974000	Weak transcription	HUVEC	blood vessel
17	chr1:45967000-45974400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:45967000-45974400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:45967000-45974400	Weak transcription	Osteobl	bone
20	chr1:45967000-45975400	Weak transcription	NH-A	brain
21	chr1:45967000-45975600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:45967000-45975800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:45967000-45977200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:45967200-45973800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:45967200-45974000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:45967200-45974000	Weak transcription	Placenta	Placenta
27	chr1:45967200-45975200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:45967200-45975400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:45967200-45975400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:45967200-45975600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:45967200-45975600	Weak transcription	Psoas Muscle	Psoas
32	chr1:45967200-45975800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:45967200-45976200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr1:45967200-45976200	Weak transcription	Fetal Lung	lung
35	chr1:45967400-45973800	Weak transcription	Left Ventricle	heart
36	chr1:45967400-45974000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:45967400-45974200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:45967400-45974200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:45967400-45974200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:45967400-45974400	Weak transcription	Fetal Kidney	kidney
41	chr1:45967400-45975600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:45967400-45975800	Weak transcription	Stomach Mucosa	stomach
43	chr1:45967600-45973800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:45967600-45973800	Weak transcription	Right Atrium	heart
45	chr1:45967600-45974000	Weak transcription	Gastric	stomach
46	chr1:45967600-45974400	Weak transcription	Esophagus	oesophagus
47	chr1:45968200-45974200	Weak transcription	Pancreas	Pancrea
48	chr1:45970400-45973800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:45971600-45985000	Strong transcription	Fetal Stomach	stomach
50	chr1:45971800-45974400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links