Variant report

Variant	rs10220835
Chromosome Location	chr15:52436615-52436616
allele	A/G
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	TEAD4	chr15:52435977-52436750	SK-N-SH	brain:	n/a	n/a
2	TEAD4	chr15:52435901-52436799	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr15:52435851-52437334	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr15:52435845-52436631	U87	brain:	n/a	n/a
5	RCOR1	chr15:52435771-52437402	IMR90	lung:	n/a	n/a
6	TCF12	chr15:52435738-52437411	SK-N-SH	brain:	n/a	n/a
7	RCOR1	chr15:52436084-52436702	Hela-S3	cervix:	n/a	n/a
8	JUND	chr15:52435960-52436724	SK-N-SH	brain:	n/a	chr15:52436307-52436318
9	POLR2A	chr15:52435845-52436681	U87	brain:	n/a	n/a
10	GATA3	chr15:52435895-52436725	SK-N-SH	brain:	n/a	chr15:52435922-52435943 chr15:52435927-52435936
11	NFIC	chr15:52435908-52436710	SK-N-SH	brain:	n/a	n/a
12	FOSL2	chr15:52435930-52437356	SK-N-SH	brain:	n/a	n/a
13	EP300	chr15:52435944-52436712	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr15:52435814-52437236	Hela-S3	cervix:	n/a	n/a
15	EP300	chr15:52435793-52436703	SK-N-SH	brain:	n/a	n/a
16	MAZ	chr15:52436002-52436786	IMR90	lung:	n/a	n/a
17	PBX3	chr15:52435930-52436626	SK-N-SH	brain:	n/a	chr15:52436176-52436196
18	GATA3	chr15:52435830-52437376	SK-N-SH	brain:	n/a	chr15:52435922-52435943 chr15:52435927-52435936
19	RXRA	chr15:52436011-52436691	SK-N-SH	brain:	n/a	n/a
20	STAT3	chr15:52435881-52436627	Hela-S3	cervix:	n/a	chr15:52436026-52436037 chr15:52436202-52436210
21	PBX3	chr15:52435871-52436657	SK-N-SH	brain:	n/a	chr15:52436176-52436196
22	JUND	chr15:52435749-52437338	SK-N-SH	brain:	n/a	chr15:52436307-52436318
23	JUND	chr15:52435914-52436728	SK-N-SH	brain:	n/a	chr15:52436307-52436318
24	MAX	chr15:52435899-52436648	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr15:52435436-52436773	U87	brain:	n/a	n/a
26	POLR2A	chr15:52435340-52436752	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52433182..52434903-chr15:52435277..52437876,2	MCF-7	breast:

Variant related genes	Relation type
GNB5	TF binding region
ENSG00000069966	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10083575	0.84[YRI][hapmap]
rs10152503	0.81[AFR][1000 genomes]
rs2470592	1.00[MEX][hapmap]
rs55678152	1.00[AMR][1000 genomes]
rs56254654	1.00[AMR][1000 genomes]
rs56709149	1.00[AMR][1000 genomes]
rs56783306	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59415316	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59694167	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59987655	1.00[AMR][1000 genomes]
rs60525483	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74015611	1.00[AMR][1000 genomes]
rs74015613	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74015616	1.00[AMR][1000 genomes]
rs8035343	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10220835	PLA2G4F	trans	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52407600-52441600	Weak transcription	Fetal Lung	lung
2	chr15:52407800-52440400	Weak transcription	Brain Substantia Nigra	brain
3	chr15:52410200-52441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:52410600-52441400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:52412000-52441200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:52422600-52457600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:52423000-52436800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:52423000-52458200	Weak transcription	Dnd41	blood
9	chr15:52424000-52441200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:52427400-52441600	Weak transcription	Esophagus	oesophagus
11	chr15:52428800-52440600	Weak transcription	Spleen	Spleen
12	chr15:52429000-52446400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:52429000-52447200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:52429200-52447400	Strong transcription	Primary T cells from cord blood	blood
15	chr15:52429600-52438400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:52429600-52440600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
18	chr15:52430000-52440800	Weak transcription	Brain Anterior Caudate	brain
19	chr15:52430000-52441400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:52430000-52442800	Weak transcription	Fetal Heart	heart
21	chr15:52430000-52445800	Weak transcription	Small Intestine	intestine
22	chr15:52430200-52437000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:52430200-52438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:52430200-52440600	Weak transcription	Fetal Intestine Small	intestine
25	chr15:52430200-52441000	Weak transcription	Gastric	stomach
26	chr15:52430200-52441800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:52430200-52442800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr15:52430200-52442800	Weak transcription	Right Ventricle	heart
29	chr15:52430200-52444800	Weak transcription	Left Ventricle	heart
30	chr15:52430200-52446600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr15:52430200-52457800	Weak transcription	Fetal Intestine Large	intestine
32	chr15:52430400-52441200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr15:52431000-52446200	Strong transcription	Primary B cells from cord blood	blood
34	chr15:52431200-52437200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:52431400-52446600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:52432200-52438600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr15:52432200-52443000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr15:52432200-52445400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:52432200-52453800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:52432200-52455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:52432200-52455200	Weak transcription	Colonic Mucosa	Colon
42	chr15:52432400-52439400	Weak transcription	Colon Smooth Muscle	Colon
43	chr15:52432400-52440400	Weak transcription	Adipose Nuclei	Adipose
44	chr15:52432600-52436800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:52432600-52441000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:52432600-52441600	Weak transcription	Brain Angular Gyrus	brain
47	chr15:52432800-52437000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:52433200-52437800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:52433400-52436800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:52434800-52437000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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