Variant report

Variant	rs3762472
Chromosome Location	chr2:99770393-99770394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:99770271-99772617	K562	blood:	n/a	n/a
2	POLR2A	chr2:99769530-99772432	PBDE	blood:	n/a	n/a
3	MXI1	chr2:99770301-99772778	SK-N-SH	brain:	n/a	n/a
4	JUN	chr2:99770177-99772090	K562	blood:	n/a	n/a
5	POLR2A	chr2:99770091-99772586	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr2:99770348-99772495	MCF10A-Er-Src	breast:	n/a	n/a
7	HCFC1	chr2:99770001-99772528	Hela-S3	cervix:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:99754528..99760418-chr2:99769364..99773305,11	K562	blood:
2	chr2:99767297..99778137-chr2:99793643..99800044,16	MCF-7	breast:
3	chr2:99769587..99774574-chr2:99795787..99799597,12	MCF-7	breast:
4	chr2:99769803..99772533-chr2:99952128..99954259,2	MCF-7	breast:
5	chr2:99756639..99759461-chr2:99768691..99772730,10	MCF-7	breast:
6	chr2:99769128..99773388-chr2:99951603..99955259,4	K562	blood:
7	chr2:99768084..99772423-chr2:99795960..99799744,7	K562	blood:
8	chr2:99767233..99772869-chr2:99793831..99799744,8	K562	blood:
9	chr2:99770250..99773199-chr2:99783967..99787710,4	MCF-7	breast:
10	chr2:99769755..99772454-chr2:99953389..99955420,3	K562	blood:
11	chr2:99755030..99760884-chr2:99769021..99772906,10	K562	blood:

No data

Variant related genes	Relation type
LIPT1	TF binding region
ENSG00000273155	TF binding region
ENSG00000135951	Chromatin interaction
ENSG00000115514	Chromatin interaction
ENSG00000185414	Chromatin interaction
ENSG00000241962	Chromatin interaction
ENSG00000273045	Chromatin interaction
ENSG00000158417	Chromatin interaction
ENSG00000158411	Chromatin interaction

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

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

rs_ID	r²[population]
rs10496334	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10496335	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123760	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11123767	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123768	0.93[EUR][1000 genomes]
rs11526114	0.86[EUR][1000 genomes]
rs12233087	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12620997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1586434	0.86[EUR][1000 genomes]
rs17020569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17022180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17022249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28785294	1.00[EUR][1000 genomes]
rs28794804	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34751553	0.81[ASN][1000 genomes]
rs35071324	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35458525	0.81[ASN][1000 genomes]
rs3791211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4850895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[ASN][1000 genomes]
rs56691336	0.81[ASN][1000 genomes]
rs56926889	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57273701	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57743480	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58595226	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58635701	0.93[EUR][1000 genomes]
rs58745514	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59252741	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59506582	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60056452	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60516303	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs60653099	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719145	0.86[EUR][1000 genomes]
rs6746969	0.86[EUR][1000 genomes]
rs6748497	0.86[EUR][1000 genomes]
rs6749198	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7568749	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608938	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs9752510	0.86[EUR][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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv535839	chr2:99742621-99793747	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3762472	ENSG00000144182	cis	multi-tissue	Pritchard
rs3762472	LIPT1	cis	multi-tissue	Pritchard

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99758600-99770400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:99758600-99770400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:99758600-99770600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:99758600-99770600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:99758800-99770400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:99758800-99770600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:99759000-99770400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:99759000-99770400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:99759000-99770400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:99759000-99770400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr2:99759000-99770400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:99759000-99770400	Weak transcription	Brain Anterior Caudate	brain
13	chr2:99759000-99770600	Weak transcription	Fetal Kidney	kidney
14	chr2:99759200-99770400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:99759200-99770400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:99759200-99770400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:99759200-99770400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:99763400-99770400	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr2:99764600-99770400	Weak transcription	Psoas Muscle	Psoas
20	chr2:99768000-99770400	Weak transcription	Primary B cells from cord blood	blood
21	chr2:99768200-99770400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr2:99768600-99770400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr2:99768600-99770600	Enhancers	Fetal Intestine Large	intestine
24	chr2:99769000-99770400	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr2:99769200-99770400	Weak transcription	Fetal Stomach	stomach
26	chr2:99769200-99770400	Weak transcription	Pancreas	Pancrea
27	chr2:99769200-99770600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:99769200-99770600	Enhancers	Fetal Intestine Small	intestine
29	chr2:99769200-99770600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr2:99769400-99770400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:99769400-99770600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr2:99769600-99770400	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr2:99769600-99770400	Enhancers	Brain Cingulate Gyrus	brain
34	chr2:99769600-99770600	Enhancers	Brain Angular Gyrus	brain
35	chr2:99769800-99770400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:99769800-99770400	Enhancers	Liver	Liver
37	chr2:99769800-99770400	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr2:99769800-99770600	Enhancers	Primary T cells from cord blood	blood
39	chr2:99769800-99770800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:99769800-99771000	Flanking Active TSS	K562	blood
41	chr2:99770000-99770400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:99770000-99770400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr2:99770000-99770400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:99770000-99770400	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr2:99770000-99770400	Enhancers	NHEK	skin
46	chr2:99770000-99770600	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr2:99770000-99770800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr2:99770200-99770400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:99770200-99770400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:99770200-99770400	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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