Variant report

Variant	rs1979552
Chromosome Location	chr15:59466779-59466780
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	POLR2A	chr15:59466648-59467356	GM12891	blood:	n/a	n/a
2	POLR2A	chr15:59466457-59467517	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:59466249-59466895	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr15:59466618-59467148	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:59466654-59467393	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr15:59466775-59467901	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr15:59466550-59467264	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr15:59465597-59468147	A549	lung:	n/a	n/a
9	EGR1	chr15:59466700-59466908	K562	blood:	n/a	chr15:59466800-59466815 chr15:59466802-59466813 chr15:59466801-59466814
10	POLR2A	chr15:59466567-59467300	GM12892	blood:	n/a	n/a
11	POLR2A	chr15:59466437-59466998	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr15:59466688-59467450	GM12891	blood:	n/a	n/a
13	POLR2A	chr15:59466648-59466811	Hela-S3	cervix:	n/a	n/a
14	SMC3	chr15:59466554-59467974	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr15:59466324-59467906	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59464898..59467094-chr15:59764802..59766481,2	K562	blood:

Variant related genes	Relation type
MIR2116	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10775168	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071409	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071410	1.00[ASN][1000 genomes]
rs11574500	1.00[ASN][1000 genomes]
rs11630246	1.00[ASN][1000 genomes]
rs13498	1.00[ASN][1000 genomes]
rs1486877	1.00[ASN][1000 genomes]
rs16941077	1.00[ASN][1000 genomes]
rs17269496	1.00[ASN][1000 genomes]
rs17269503	1.00[ASN][1000 genomes]
rs1967063	0.81[AFR][1000 genomes]
rs28739025	1.00[ASN][1000 genomes]
rs4775121	1.00[ASN][1000 genomes]
rs57164516	1.00[ASN][1000 genomes]
rs60440107	1.00[ASN][1000 genomes]
rs61055592	1.00[ASN][1000 genomes]
rs6494072	1.00[ASN][1000 genomes]
rs7173787	1.00[ASN][1000 genomes]
rs7174992	1.00[ASN][1000 genomes]
rs7175697	1.00[ASN][1000 genomes]
rs74017367	1.00[ASN][1000 genomes]
rs8036093	1.00[ASN][1000 genomes]
rs8041633	1.00[ASN][1000 genomes]
rs923242	0.87[AFR][1000 genomes]
rs931346	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59431800-59467200	Weak transcription	Fetal Brain Female	brain
2	chr15:59434200-59467000	Strong transcription	Rectal Mucosa Donor 31	rectum
3	chr15:59436000-59473000	Weak transcription	Brain Germinal Matrix	brain
4	chr15:59437800-59484400	Weak transcription	Fetal Brain Male	brain
5	chr15:59445600-59479600	Weak transcription	Fetal Kidney	kidney
6	chr15:59445800-59467000	Weak transcription	Fetal Heart	heart
7	chr15:59451200-59473600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:59451400-59470400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:59451600-59474600	Weak transcription	Psoas Muscle	Psoas
10	chr15:59453400-59467200	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:59453800-59470000	Weak transcription	Right Ventricle	heart
12	chr15:59454000-59482000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:59454800-59471600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:59455200-59467200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:59458000-59470000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr15:59458600-59473800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr15:59459200-59466800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr15:59459400-59467000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:59461000-59474800	Strong transcription	Liver	Liver
20	chr15:59461200-59467000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:59461400-59466800	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:59461800-59467200	Strong transcription	Hela-S3	cervix
23	chr15:59462000-59466800	Strong transcription	Fetal Intestine Small	intestine
24	chr15:59462000-59467000	Strong transcription	Fetal Intestine Large	intestine
25	chr15:59462000-59467200	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr15:59462400-59467200	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:59462600-59466800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr15:59462800-59466800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr15:59462800-59467000	Weak transcription	Right Atrium	heart
30	chr15:59463000-59466800	Weak transcription	Adipose Nuclei	Adipose
31	chr15:59463000-59467000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:59463200-59466800	Weak transcription	Brain Anterior Caudate	brain
33	chr15:59463200-59466800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:59463200-59467000	Strong transcription	A549	lung
35	chr15:59463200-59468800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:59463200-59473000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:59463400-59466800	Strong transcription	HSMM	muscle
38	chr15:59463400-59468600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:59463600-59466800	Strong transcription	Primary B cells from cord blood	blood
40	chr15:59463600-59466800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:59463600-59466800	Strong transcription	Placenta	Placenta
42	chr15:59463600-59467000	Weak transcription	Fetal Thymus	thymus
43	chr15:59463600-59468600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:59463600-59469000	Weak transcription	Colonic Mucosa	Colon
45	chr15:59463600-59470200	Weak transcription	Esophagus	oesophagus
46	chr15:59463600-59471800	Weak transcription	Small Intestine	intestine
47	chr15:59463800-59470200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:59464000-59469600	Weak transcription	Spleen	Spleen
49	chr15:59464000-59472800	Weak transcription	Ovary	ovary
50	chr15:59464200-59466800	Weak transcription	Primary monocytes fromperipheralblood	blood

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