Variant report

Variant	rs4076055
Chromosome Location	chr2:11889385-11889386
allele	A/C
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	chr2:11886620-11891581	GM12878	blood:	n/a	n/a
2	ELF1	chr2:11889276-11889745	GM12878	blood:	n/a	chr2:11889577-11889588
3	EBF1	chr2:11889240-11889534	GM12878	blood:	n/a	n/a
4	RUNX3	chr2:11889166-11891510	GM12878	blood:	n/a	n/a
5	EP300	chr2:11888661-11891529	GM12878	blood:	n/a	chr2:11889573-11889587 chr2:11889511-11889527 chr2:11889056-11889070 chr2:11889113-11889122
6	WRNIP1	chr2:11887983-11890899	GM12878	blood:	n/a	n/a
7	RFX5	chr2:11889181-11889445	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:11886595-11892488	MCF10A-Er-Src	breast:	n/a	n/a
9	CHD1	chr2:11886735-11891594	GM12878	blood:	n/a	n/a
10	CHD2	chr2:11888090-11891444	GM12878	blood:	n/a	n/a
11	SPI1	chr2:11889377-11889741	GM12878	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
12	ZBTB7A	chr2:11889374-11889551	K562	blood:	n/a	n/a
13	POLR2A	chr2:11889153-11891585	GM12878	blood:	n/a	n/a
14	RCOR1	chr2:11888262-11891527	GM12878	blood:	n/a	n/a
15	MAZ	chr2:11888474-11891368	GM12878	blood:	n/a	chr2:11890696-11890706 chr2:11890692-11890707 chr2:11890695-11890706 chr2:11890695-11890705 chr2:11890697-11890706 chr2:11890694-11890709 chr2:11890694-11890707 chr2:11890696-11890705 chr2:11890694-11890707 chr2:11890695-11890706 chr2:11888946-11888956 chr2:11890694-11890707 chr2:11890696-11890705 chr2:11888796-11888806 chr2:11890695-11890706 chr2:11890697-11890704
16	SPI1	chr2:11889111-11890020	GM12878	blood:	n/a	chr2:11889572-11889579 chr2:11889570-11889583 chr2:11889578-11889585 chr2:11889576-11889589 chr2:11889576-11889589
17	POU2F2	chr2:11889158-11891531	GM12878	blood:	n/a	chr2:11890115-11890129 chr2:11890117-11890126 chr2:11891211-11891224 chr2:11890116-11890126 chr2:11890205-11890217 chr2:11890118-11890125 chr2:11890116-11890126 chr2:11890115-11890127
18	POLR2A	chr2:11888404-11891507	GM18505	blood:	n/a	n/a
19	POLR2A	chr2:11889324-11889705	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:11889317-11891423	GM15510	blood:	n/a	n/a
21	POLR2A	chr2:11889241-11889609	K562	blood:	n/a	n/a
22	POLR2A	chr2:11887260-11891538	GM12891	blood:	n/a	n/a
23	POLR2A	chr2:11888165-11891554	GM12878	blood:	n/a	n/a
24	POLR2A	chr2:11886566-11891563	GM12878	blood:	n/a	n/a
25	MAX	chr2:11889230-11891382	GM12878	blood:	n/a	chr2:11890696-11890706 chr2:11890692-11890707 chr2:11890695-11890706 chr2:11890695-11890705 chr2:11890697-11890706 chr2:11890694-11890709 chr2:11890694-11890707 chr2:11890716-11890726 chr2:11890696-11890705 chr2:11890694-11890707 chr2:11890695-11890706 chr2:11890694-11890707 chr2:11890696-11890705 chr2:11890695-11890706 chr2:11890694-11890704 chr2:11890697-11890704

No.	Distal block	Cell Line	Cell type
1	chr2:11881178..11885762-chr2:11886043..11889477,7	MCF-7	breast:
2	chr2:11887777..11889810-chr2:11903193..11905347,2	K562	blood:
3	chr2:11827642..11829503-chr2:11889193..11891335,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230790	TF binding region
ENSG00000230790	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1006538	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10169802	1.00[ASN][1000 genomes]
rs10191952	0.81[CHB][hapmap]
rs10191977	0.81[CHB][hapmap]
rs10192566	1.00[ASN][1000 genomes]
rs10205312	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10205400	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10207506	0.99[ASN][1000 genomes]
rs10208679	0.99[ASN][1000 genomes]
rs10209969	0.91[ASN][1000 genomes]
rs11676086	0.99[ASN][1000 genomes]
rs11693809	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11897144	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13407101	0.93[ASN][1000 genomes]
rs13409154	0.99[ASN][1000 genomes]
rs13412852	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1469952	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17603420	0.83[JPT][hapmap]
rs2278513	0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2358041	0.89[ASN][1000 genomes]
rs2358042	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2358126	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs2577264	0.87[MEX][hapmap];1.00[YRI][hapmap]
rs4129757	0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs4315495	0.99[ASN][1000 genomes]
rs4669778	0.81[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs62113306	0.97[ASN][1000 genomes]
rs6717910	0.81[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6731096	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72773994	0.91[ASN][1000 genomes]
rs7595221	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs873358	0.99[ASN][1000 genomes]
rs893342	0.92[ASN][1000 genomes]
rs893349	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv580973	chr2:11864946-11898931	Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv580974	chr2:11867841-11898931	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4076055	LPIN1	cis	parietal	SCAN
rs4076055	LPIN1	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11887000-11890400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:11887000-11891600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:11887200-11889400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr2:11887200-11890400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr2:11887400-11889600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:11887400-11889600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:11887400-11890400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:11887400-11890400	Enhancers	Spleen	Spleen
9	chr2:11887400-11890600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr2:11887600-11890400	Enhancers	Fetal Muscle Trunk	muscle
11	chr2:11887600-11890600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:11887600-11891200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr2:11887600-11891400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:11887800-11889600	Flanking Active TSS	HepG2	liver
15	chr2:11887800-11889800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr2:11887800-11889800	Flanking Active TSS	NHEK	skin
17	chr2:11887800-11890000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:11887800-11891400	Enhancers	Fetal Muscle Leg	muscle
19	chr2:11887800-11894000	Enhancers	Primary B cells from peripheral blood	blood
20	chr2:11888000-11889400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:11888000-11889400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:11888000-11889400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:11888000-11889600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:11888000-11889600	Flanking Active TSS	Right Ventricle	heart
25	chr2:11888000-11890000	Weak transcription	HSMMtube	muscle
26	chr2:11888000-11890400	Enhancers	Fetal Brain Male	brain
27	chr2:11888000-11891400	Enhancers	Primary B cells from cord blood	blood
28	chr2:11888000-11891600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr2:11888000-11891600	Flanking Active TSS	GM12878-XiMat	blood
30	chr2:11888000-11891800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:11888200-11889400	Weak transcription	Fetal Heart	heart
32	chr2:11888200-11889800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:11888200-11890000	Flanking Active TSS	NHLF	lung
34	chr2:11888200-11890600	Weak transcription	Osteobl	bone
35	chr2:11888200-11891200	Enhancers	Brain Cingulate Gyrus	brain
36	chr2:11888200-11891400	Enhancers	Brain Angular Gyrus	brain
37	chr2:11888400-11889400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:11888400-11889600	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr2:11888400-11889800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:11888400-11889800	Enhancers	Gastric	stomach
41	chr2:11888400-11890000	Enhancers	Liver	Liver
42	chr2:11888400-11890200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:11888400-11890200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr2:11888400-11890400	Enhancers	Lung	lung
45	chr2:11888400-11890600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:11888400-11890600	Enhancers	Adipose Nuclei	Adipose
47	chr2:11888400-11890600	Enhancers	Brain Germinal Matrix	brain
48	chr2:11888400-11890800	Weak transcription	Placenta	Placenta
49	chr2:11888400-11890800	Enhancers	Ovary	ovary
50	chr2:11888400-11891000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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