Variant report

Variant	rs72478602
Chromosome Location	chr1:45964987-45964988
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:45964980-45965130	GM12864	blood:	n/a	n/a
2	CTCF	chr1:45964960-45965110	WERI-Rb-1	eye:	n/a	n/a
3	HCFC1	chr1:45964803-45966980	Hela-S3	cervix:	n/a	n/a
4	ZBTB7A	chr1:45964963-45965413	K562	blood:	n/a	n/a
5	MXI1	chr1:45964964-45967174	SK-N-SH	brain:	n/a	n/a
6	SMARCC2	chr1:45964799-45966165	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:45964582-45967225	HepG2	liver:	n/a	n/a
8	MTA3	chr1:45964977-45966341	GM12878	blood:	n/a	n/a
9	CTCF	chr1:45964980-45965130	GM06990	blood:	n/a	n/a
10	WRNIP1	chr1:45964987-45966163	GM12878	blood:	n/a	n/a
11	CTCF	chr1:45964958-45965214	K562	blood:	n/a	n/a
12	CTCF	chr1:45964960-45965110	HUVEC	blood vessel:	n/a	n/a
13	CTCF	chr1:45964980-45965130	HEK293	kidney:	n/a	n/a
14	POLR2A	chr1:45964960-45966439	H1-hESC	embryonic stem cell:	n/a	n/a
15	SMARCC1	chr1:45964918-45966156	Hela-S3	cervix:	n/a	n/a
16	NR2F2	chr1:45964961-45966314	K562	blood:	n/a	n/a
17	CTCF	chr1:45964940-45965090	GM12871	blood:	n/a	n/a
18	CTCF	chr1:45964980-45965130	GM12872	blood:	n/a	n/a
19	SREBP1	chr1:45964570-45967128	GM12878	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45804114..45807301-chr1:45961577..45967419,8	K562	blood:
2	chr1:45185969..45188598-chr1:45964540..45967567,4	K562	blood:
3	chr1:45283510..45287262-chr1:45964108..45968951,6	K562	blood:
4	chr1:45806085..45807923-chr1:45963911..45966246,2	MCF-7	breast:
5	chr1:45768003..45772070-chr1:45964648..45967315,5	K562	blood:
6	chr1:45963397..45969763-chr1:46047572..46053150,23	K562	blood:
7	chr1:45963437..45971807-chr1:46047572..46053150,22	K562	blood:
8	chr1:45265558..45267516-chr1:45964222..45967034,2	K562	blood:
9	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:
10	chr1:45964150..45967582-chr1:46014583..46018871,5	K562	blood:
11	chr1:45272934..45277358-chr1:45964626..45967668,4	K562	blood:
12	chr1:45284392..45287262-chr1:45964108..45967526,3	K562	blood:

No data

Variant related genes	Relation type
CCDC163P	TF binding region
MMACHC	TF binding region
ENSG00000132781	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000132780	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12065695	1.00[ASN][1000 genomes]
rs12066809	1.00[ASN][1000 genomes]
rs12070890	1.00[ASN][1000 genomes]
rs12083690	1.00[ASN][1000 genomes]
rs16832559	1.00[ASN][1000 genomes]
rs1855621	1.00[ASN][1000 genomes]
rs28674795	1.00[ASN][1000 genomes]
rs2934860	1.00[ASN][1000 genomes]
rs2934861	1.00[ASN][1000 genomes]
rs2934863	1.00[ASN][1000 genomes]
rs2934864	1.00[ASN][1000 genomes]
rs2991965	1.00[ASN][1000 genomes]
rs2991967	1.00[ASN][1000 genomes]
rs2991969	1.00[ASN][1000 genomes]
rs2991984	1.00[ASN][1000 genomes]
rs2993256	1.00[ASN][1000 genomes]
rs2993260	1.00[ASN][1000 genomes]
rs2993261	1.00[ASN][1000 genomes]
rs3014222	1.00[ASN][1000 genomes]
rs3014223	1.00[ASN][1000 genomes]
rs3014224	1.00[ASN][1000 genomes]
rs3014226	1.00[ASN][1000 genomes]
rs35103566	1.00[ASN][1000 genomes]
rs36053912	1.00[ASN][1000 genomes]
rs59050426	1.00[ASN][1000 genomes]
rs60347972	1.00[ASN][1000 genomes]
rs6664588	1.00[ASN][1000 genomes]
rs6671347	1.00[ASN][1000 genomes]
rs6677135	1.00[ASN][1000 genomes]
rs6699702	1.00[ASN][1000 genomes]
rs72900311	1.00[ASN][1000 genomes]
rs7412911	1.00[ASN][1000 genomes]
rs7536559	1.00[ASN][1000 genomes]
rs7550744	1.00[ASN][1000 genomes]
rs9429080	1.00[ASN][1000 genomes]
rs9429083	1.00[ASN][1000 genomes]
rs9429164	1.00[ASN][1000 genomes]
rs9429165	1.00[ASN][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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45956800-45965000	Weak transcription	Gastric	stomach
2	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
3	chr1:45957400-45965200	Weak transcription	HSMM	muscle
4	chr1:45957600-45965000	Weak transcription	Psoas Muscle	Psoas
5	chr1:45957800-45965000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:45957800-45965000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:45962400-45965000	Weak transcription	Right Atrium	heart
8	chr1:45962600-45965000	Weak transcription	Left Ventricle	heart
9	chr1:45963200-45965200	Weak transcription	Aorta	Aorta
10	chr1:45964000-45965000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:45964000-45965000	Enhancers	Liver	Liver
12	chr1:45964000-45965000	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:45964000-45965000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:45964000-45965000	Flanking Active TSS	HepG2	liver
15	chr1:45964200-45965000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:45964200-45965000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:45964200-45965000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr1:45964200-45965000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:45964200-45965000	Enhancers	Fetal Stomach	stomach
20	chr1:45964200-45965200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:45964400-45965000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:45964400-45965000	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:45964400-45965000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:45964400-45965000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr1:45964400-45965000	Enhancers	Brain Angular Gyrus	brain
26	chr1:45964400-45965000	Enhancers	Fetal Thymus	thymus
27	chr1:45964400-45965200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:45964400-45965400	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr1:45964400-45965400	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr1:45964400-45965400	Flanking Active TSS	Dnd41	blood
31	chr1:45964400-45966600	Active TSS	A549	lung
32	chr1:45964400-45966800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:45964600-45965000	Enhancers	H9 Cell Line	embryonic stem cell
34	chr1:45964600-45965000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:45964600-45965000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:45964600-45965000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:45964600-45965000	Enhancers	Primary B cells from cord blood	blood
38	chr1:45964600-45965000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:45964600-45965000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:45964600-45965000	Enhancers	Brain Germinal Matrix	brain
41	chr1:45964600-45965000	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr1:45964600-45965000	Enhancers	Fetal Intestine Large	intestine
43	chr1:45964600-45965000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:45964600-45965000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr1:45964600-45965000	Enhancers	HUVEC	blood vessel
46	chr1:45964600-45965200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:45964600-45965200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:45964600-45965200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:45964600-45965200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:45964600-45965200	Enhancers	Colon Smooth Muscle	Colon

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