Variant report

Variant	rs13412852
Chromosome Location	chr2:11914941-11914942
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	chr2:11914782-11914947	Hela-S3	cervix:	n/a	n/a
2	EP300	chr2:11912906-11915032	SK-N-SH	brain:	n/a	chr2:11912969-11912976
3	POLR2A	chr2:11914456-11914993	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11906537..11909514-chr2:11912948..11915270,2	MCF-7	breast:
2	chr2:11902752..11905515-chr2:11914841..11917001,2	K562	blood:

Variant related genes	Relation type
LPIN1	TF binding region
ENSG00000265056	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1006538	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10169802	0.89[ASN][1000 genomes]
rs10192566	0.89[ASN][1000 genomes]
rs10205312	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10205400	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs10207506	0.90[ASN][1000 genomes]
rs10208679	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10209969	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11676086	0.90[ASN][1000 genomes]
rs11690125	1.00[ASW][hapmap]
rs11693809	0.89[ASN][1000 genomes]
rs11695610	1.00[ASW][hapmap]
rs11897144	0.92[ASN][1000 genomes]
rs13384037	0.90[LWK][hapmap]
rs13390952	0.90[LWK][hapmap]
rs13407101	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13409154	0.90[ASN][1000 genomes]
rs1469952	0.94[ASN][1000 genomes]
rs17603197	1.00[ASW][hapmap]
rs17603420	0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2099597	0.84[ASN][1000 genomes]
rs2278513	0.88[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2358041	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358042	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358126	0.89[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4076055	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4129757	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs4315495	0.90[ASN][1000 genomes]
rs4669778	0.89[CHD][hapmap]
rs62113306	0.86[ASN][1000 genomes]
rs6717910	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6731096	0.86[ASN][1000 genomes]
rs6757892	0.85[ASN][1000 genomes]
rs72773994	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7561070	0.85[ASN][1000 genomes]
rs7595221	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7607755	0.85[ASN][1000 genomes]
rs873358	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs893342	0.97[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13412852	FAM84A	cis	cerebellum	SCAN
rs13412852	LPIN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11888400-11916400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:11895000-11918200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:11900600-11918000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:11901200-11915000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:11901800-11918600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:11903000-11915000	Strong transcription	NHEK	skin
7	chr2:11903200-11915000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:11905000-11915400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:11905200-11915000	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:11905200-11919000	Weak transcription	Stomach Mucosa	stomach
11	chr2:11905400-11915600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:11905400-11916600	Strong transcription	Stomach Smooth Muscle	stomach
13	chr2:11905400-11916800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:11905600-11915000	Strong transcription	Adipose Nuclei	Adipose
15	chr2:11905800-11915200	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:11906000-11917400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:11906400-11924600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:11906600-11924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:11906800-11924600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:11907200-11916800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:11908000-11919000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:11908600-11917600	Strong transcription	K562	blood
23	chr2:11909000-11915600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:11909000-11919000	Strong transcription	HMEC	breast
25	chr2:11909600-11915400	Strong transcription	Fetal Muscle Leg	muscle
26	chr2:11909600-11916600	Strong transcription	Fetal Stomach	stomach
27	chr2:11909800-11915000	Strong transcription	Fetal Intestine Small	intestine
28	chr2:11909800-11915400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr2:11909800-11915800	Strong transcription	Brain Hippocampus Middle	brain
30	chr2:11909800-11915800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr2:11910000-11915000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:11910000-11915000	Strong transcription	Gastric	stomach
33	chr2:11910000-11915000	Strong transcription	Lung	lung
34	chr2:11910000-11915200	Strong transcription	Ovary	ovary
35	chr2:11910000-11915400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr2:11910000-11915600	Strong transcription	Fetal Thymus	thymus
37	chr2:11910000-11917400	Strong transcription	HepG2	liver
38	chr2:11910000-11918400	Strong transcription	Thymus	Thymus
39	chr2:11910200-11915200	Strong transcription	Placenta	Placenta
40	chr2:11910200-11915600	Strong transcription	Brain Germinal Matrix	brain
41	chr2:11910200-11916400	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr2:11910800-11915200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:11911000-11915000	Strong transcription	Fetal Intestine Large	intestine
44	chr2:11911000-11915600	Strong transcription	Brain Cingulate Gyrus	brain
45	chr2:11911400-11915000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:11911600-11915400	Strong transcription	HSMMtube	muscle
47	chr2:11911800-11915400	Strong transcription	Brain Anterior Caudate	brain
48	chr2:11911800-11918200	Weak transcription	Small Intestine	intestine
49	chr2:11912000-11915600	Weak transcription	Hela-S3	cervix
50	chr2:11912000-11919000	Weak transcription	A549	lung

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