Variant report

Variant	rs9963611
Chromosome Location	chr18:29675157-29675158
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	KAP1	chr18:29675074-29676117	HEK293	kidney:	n/a	n/a
2	POLR2A	chr18:29675157-29675279	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr18:29671561-29677909	K562	blood:	n/a	n/a
4	POLR2A	chr18:29675057-29675490	GM12878	blood:	n/a	n/a
5	SETDB1	chr18:29675102-29675641	U2OS	brain:	n/a	n/a
6	KAP1	chr18:29675096-29675525	U2OS	brain:	n/a	n/a
7	POLR2A	chr18:29675063-29675428	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29671668..29674127-chr18:29674569..29677601,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265008	TF binding region
ENSG00000265008	Chromatin interaction
ENSG00000134758	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs16962691	1.00[AFR][1000 genomes]
rs28376309	1.00[AMR][1000 genomes]
rs28429168	1.00[AMR][1000 genomes]
rs28464735	1.00[AMR][1000 genomes]
rs28478378	1.00[AMR][1000 genomes]
rs28505817	1.00[AMR][1000 genomes]
rs28538314	1.00[AMR][1000 genomes]
rs28556958	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28596473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28727388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28822754	1.00[AMR][1000 genomes]
rs7239030	1.00[AMR][1000 genomes]
rs73413957	1.00[AMR][1000 genomes]
rs73413961	1.00[AMR][1000 genomes]
rs8091726	1.00[AFR][1000 genomes]
rs9949793	1.00[AMR][1000 genomes]
rs9954827	1.00[AMR][1000 genomes]
rs9954966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9967305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909523	chr18:29645496-29679922	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1055457	chr18:29654978-29677371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29672600-29676000	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr18:29673400-29692800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:29673400-29713800	Weak transcription	Spleen	Spleen
4	chr18:29673600-29675400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr18:29673600-29675400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr18:29673600-29678400	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr18:29673800-29675200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr18:29673800-29675200	Enhancers	Adipose Nuclei	Adipose
9	chr18:29673800-29675200	Enhancers	Brain Hippocampus Middle	brain
10	chr18:29673800-29675800	Weak transcription	Left Ventricle	heart
11	chr18:29673800-29675800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr18:29673800-29676400	Weak transcription	Aorta	Aorta
13	chr18:29673800-29676400	Enhancers	Brain Angular Gyrus	brain
14	chr18:29673800-29676600	Enhancers	Brain Cingulate Gyrus	brain
15	chr18:29673800-29676600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr18:29673800-29676600	Enhancers	Brain Substantia Nigra	brain
17	chr18:29673800-29676800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr18:29673800-29677000	Enhancers	Fetal Heart	heart
19	chr18:29673800-29678000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr18:29673800-29679400	Weak transcription	Gastric	stomach
21	chr18:29673800-29702000	Weak transcription	Pancreas	Pancrea
22	chr18:29673800-29714000	Weak transcription	Esophagus	oesophagus
23	chr18:29673800-29714200	Weak transcription	Ovary	ovary
24	chr18:29673800-29715200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr18:29673800-29715200	Weak transcription	Lung	lung
26	chr18:29673800-29715800	Weak transcription	Colonic Mucosa	Colon
27	chr18:29673800-29717000	Weak transcription	HSMMtube	muscle
28	chr18:29674000-29675200	Enhancers	Fetal Intestine Small	intestine
29	chr18:29674000-29675400	Enhancers	Stomach Mucosa	stomach
30	chr18:29674000-29676000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr18:29674000-29676000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr18:29674000-29676400	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr18:29674000-29677400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr18:29674000-29679000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr18:29674000-29679600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr18:29674000-29689200	Weak transcription	Right Atrium	heart
37	chr18:29674000-29692600	Weak transcription	Placenta	Placenta
38	chr18:29674000-29712000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr18:29674200-29675200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr18:29674200-29675200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr18:29674200-29675400	Transcr. at gene 5' and 3'	K562	blood
42	chr18:29674200-29676400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr18:29674200-29676400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr18:29674200-29677800	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr18:29674200-29692800	Weak transcription	HSMM	muscle
46	chr18:29674200-29693000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr18:29674400-29675200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
48	chr18:29674400-29675200	Genic enhancers	Fetal Lung	lung
49	chr18:29674400-29675400	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr18:29674400-29675400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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