Variant report

Variant	rs180875874
Chromosome Location	chr18:12989828-12989829
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:12989157-12991987	K562	blood:	n/a	n/a
2	POLR2A	chr18:12989077-12992444	GM12878	blood:	n/a	n/a
3	POLR2A	chr18:12989656-12992325	U87	brain:	n/a	n/a
4	POLR2A	chr18:12988809-12992393	GM12891	blood:	n/a	n/a
5	POLR2A	chr18:12989551-12991973	K562	blood:	n/a	n/a
6	POLR2A	chr18:12989574-12989878	HCT-116	colon:	n/a	n/a
7	POLR2A	chr18:12989647-12992015	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr18:12987789-12992309	HepG2	liver:	n/a	n/a
9	POLR2A	chr18:12989539-12992068	MCF-7	breast:	n/a	n/a
10	POLR2A	chr18:12989755-12992218	HepG2	liver:	n/a	n/a
11	POLR2A	chr18:12989181-12992009	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr18:12989665-12992592	GM12878	blood:	n/a	n/a
13	POLR2A	chr18:12989716-12991987	K562	blood:	n/a	n/a
14	E2F4	chr18:12989806-12989955	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr18:12989697-12992291	U87	brain:	n/a	n/a
16	NFATC1	chr18:12989447-12991790	GM12878	blood:	n/a	chr18:12990092-12990106
17	POLR2A	chr18:12988575-12992092	GM12892	blood:	n/a	n/a
18	POLR2A	chr18:12989410-12992090	HL-60	blood:	n/a	n/a
19	POLR2A	chr18:12989242-12989918	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr18:12989595-12989844	HepG2	liver:	n/a	n/a
21	POLR2A	chr18:12987994-12992103	K562	blood:	n/a	n/a
22	POLR2A	chr18:12988613-12991875	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr18:12989368-12992170	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12979831..12981804-chr18:12988179..12989952,2	K562	blood:
2	chr18:12988791..12990408-chr18:13028721..13030724,2	K562	blood:
3	chr18:12945719..12950670-chr18:12989123..12995651,19	K562	blood:
4	chr18:12971249..12974224-chr18:12989349..12991861,2	MCF-7	breast:
5	chr18:12944429..12952802-chr18:12987284..12998193,21	K562	blood:
6	chr18:12945869..12950267-chr18:12985686..12992743,10	MCF-7	breast:
7	chr18:12989546..12991386-chr18:13006007..13008502,2	K562	blood:

No data

Variant related genes	Relation type
CEP192	TF binding region
ENSG00000085415	Chromatin interaction
ENSG00000101639	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1062413	chr18:12988947-13039941	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv543657	chr18:12988947-13039941	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	esv3395285	chr18:12988952-12991750	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12950000-12990200	Weak transcription	Fetal Brain Male	brain
2	chr18:12951400-12990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr18:12959000-12990200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr18:12972800-12990000	Weak transcription	Brain Substantia Nigra	brain
5	chr18:12973200-12990200	Weak transcription	Small Intestine	intestine
6	chr18:12974200-12990200	Weak transcription	Brain Hippocampus Middle	brain
7	chr18:12975800-12990200	Weak transcription	Right Ventricle	heart
8	chr18:12976000-12990200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr18:12976400-12990000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr18:12976400-12990000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr18:12976400-12990000	Weak transcription	Colon Smooth Muscle	Colon
12	chr18:12976400-12990000	Weak transcription	Stomach Mucosa	stomach
13	chr18:12976400-12990200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:12976400-12990200	Weak transcription	Brain Angular Gyrus	brain
15	chr18:12976400-12990200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr18:12976400-12990200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr18:12976400-12990400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr18:12976600-12990000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr18:12976600-12990000	Weak transcription	Fetal Heart	heart
20	chr18:12976600-12990200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr18:12976600-12990200	Weak transcription	Brain Anterior Caudate	brain
22	chr18:12976600-12990200	Weak transcription	Esophagus	oesophagus
23	chr18:12976600-12990200	Weak transcription	Spleen	Spleen
24	chr18:12976600-12990400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr18:12976600-12990800	Weak transcription	Aorta	Aorta
26	chr18:12976800-12990200	Weak transcription	Fetal Lung	lung
27	chr18:12977400-12990600	Weak transcription	HSMMtube	muscle
28	chr18:12978600-12990200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr18:12978600-12990200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr18:12978600-12990200	Weak transcription	Pancreas	Pancrea
31	chr18:12978800-12990000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr18:12978800-12990000	Weak transcription	NHLF	lung
33	chr18:12979000-12990000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr18:12979000-12990000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr18:12982200-12990200	Weak transcription	Fetal Intestine Small	intestine
36	chr18:12983200-12990000	Weak transcription	Thymus	Thymus
37	chr18:12983200-12990200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr18:12983200-12990200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr18:12983400-12990200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr18:12983400-12990200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr18:12983600-12990200	Weak transcription	Gastric	stomach
42	chr18:12983600-12990200	Weak transcription	Lung	lung
43	chr18:12983600-12990400	Weak transcription	Fetal Brain Female	brain
44	chr18:12983600-12990400	Weak transcription	Fetal Stomach	stomach
45	chr18:12983800-12990000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr18:12984200-12990200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr18:12984200-12990200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr18:12984200-12990200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr18:12984200-12990200	Weak transcription	Fetal Muscle Leg	muscle
50	chr18:12984200-12990200	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links