Variant report

Variant	rs932959
Chromosome Location	chr15:41810439-41810440
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr15:41810306-41810597	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:41809984-41810509	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr15:41810189-41810539	HepG2	liver:	n/a	n/a
4	HNF4A	chr15:41810316-41810659	HepG2	liver:	n/a	n/a
5	HNF4G	chr15:41810320-41810574	HepG2	liver:	n/a	chr15:41810472-41810487
6	FOXA1	chr15:41810174-41810643	HepG2	liver:	n/a	n/a
7	YY1	chr15:41810426-41810660	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:41810073-41810504	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr15:41810312-41810539	HepG2	liver:	n/a	n/a
10	EP300	chr15:41810358-41810509	HepG2	liver:	n/a	n/a
11	SP1	chr15:41810207-41810651	HepG2	liver:	n/a	n/a
12	TEAD4	chr15:41810168-41810637	HepG2	liver:	n/a	n/a
13	TBP	chr15:41810252-41810510	HepG2	liver:	n/a	n/a
14	FOXA2	chr15:41810262-41810577	HepG2	liver:	n/a	n/a
15	POLR2A	chr15:41809529-41810814	HepG2	liver:	n/a	n/a
16	CREB1	chr15:41810116-41810666	HepG2	liver:	n/a	n/a
17	POLR2A	chr15:41810275-41810508	H1-hESC	embryonic stem cell:	n/a	n/a
18	FOXA1	chr15:41810196-41810583	HepG2	liver:	n/a	n/a
19	FOXA1	chr15:41810174-41810662	HepG2	liver:	n/a	n/a
20	ARID3A	chr15:41810295-41810629	HepG2	liver:	n/a	n/a
21	CHD2	chr15:41810343-41810521	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41805856..41809445-chr15:41809960..41813355,6	K562	blood:
2	chr15:41785345..41788204-chr15:41809016..41810718,2	K562	blood:
3	chr15:41785345..41788204-chr15:41808714..41810718,3	K562	blood:

No data

Variant related genes	Relation type
LTK	TF binding region
ENSG00000062524	Chromatin interaction
ENSG00000137825	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11070334	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2297377	0.88[CEU][hapmap]
rs2297380	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs2412615	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3743031	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv904110	chr15:41776692-41813279	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv471241	chr15:41783814-41820200	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv904112	chr15:41806658-41836234	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs932959	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs932959	RPAP1	cis	Artery Tibial	GTEx
rs932959	RPAP1	cis	Esophagus Muscularis	GTEx
rs932959	LTK	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41801800-41819000	Weak transcription	Hela-S3	cervix
2	chr15:41806200-41815400	Weak transcription	NHDF-Ad	bronchial
3	chr15:41806200-41820400	Weak transcription	HSMM	muscle
4	chr15:41806200-41822600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:41806400-41812400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:41806400-41812800	Weak transcription	Colonic Mucosa	Colon
7	chr15:41806400-41815600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:41806400-41818600	Weak transcription	Primary B cells from cord blood	blood
9	chr15:41806400-41835200	Weak transcription	Right Atrium	heart
10	chr15:41806600-41812400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr15:41806600-41812400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:41806600-41812800	Weak transcription	Osteobl	bone
13	chr15:41806600-41813200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr15:41806600-41813600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr15:41806600-41815000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr15:41806600-41817000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:41806600-41818800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:41806600-41818800	Weak transcription	GM12878-XiMat	blood
19	chr15:41806600-41819000	Weak transcription	HUVEC	blood vessel
20	chr15:41806600-41819200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr15:41806600-41824600	Weak transcription	Fetal Kidney	kidney
22	chr15:41806600-41835200	Weak transcription	Fetal Heart	heart
23	chr15:41806800-41812200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:41806800-41818200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:41806800-41818400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr15:41806800-41818600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr15:41806800-41818800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:41806800-41818800	Weak transcription	Stomach Mucosa	stomach
29	chr15:41806800-41822400	Weak transcription	NH-A	brain
30	chr15:41807000-41816400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr15:41807200-41819400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:41807200-41835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:41807600-41810800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:41808000-41829600	Strong transcription	Fetal Stomach	stomach
35	chr15:41808200-41818200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:41808200-41820600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:41808600-41810600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:41808600-41810600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:41808600-41810600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:41808600-41810600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:41808600-41812800	Strong transcription	Brain Cingulate Gyrus	brain
42	chr15:41808600-41823000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:41808600-41829200	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr15:41808600-41829600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:41808600-41835400	Weak transcription	Fetal Brain Male	brain
46	chr15:41808800-41810600	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:41808800-41810600	Strong transcription	Fetal Brain Female	brain
48	chr15:41808800-41810800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:41808800-41810800	Strong transcription	Fetal Intestine Small	intestine
50	chr15:41808800-41829600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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