Variant report

Variant	rs10496334
Chromosome Location	chr2:99796688-99796689
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:99796520-99796933	SH-SY5Y	brain:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:99782491..99787778-chr2:99795073..99800536,8	MCF-7	breast:
2	chr2:99767297..99778137-chr2:99793643..99800044,16	MCF-7	breast:
3	chr2:99768084..99772423-chr2:99795960..99799744,7	K562	blood:
4	chr2:99785439..99787050-chr2:99795016..99797039,2	MCF-7	breast:
5	chr2:99786426..99788030-chr2:99796073..99799242,3	K562	blood:
6	chr2:99773460..99775847-chr2:99795647..99797318,2	K562	blood:
7	chr2:99757575..99760395-chr2:99795675..99798209,3	K562	blood:
8	chr2:99767233..99772869-chr2:99793831..99799744,8	K562	blood:
9	chr2:99796217..99799127-chr2:100105224..100108883,4	K562	blood:
10	chr2:99769587..99774574-chr2:99795787..99799597,12	MCF-7	breast:
11	chr2:99755178..99760444-chr2:99795813..99800130,7	MCF-7	breast:
12	chr2:99796467..99798602-chr2:99952178..99954116,2	K562	blood:
13	chr2:99796197..99799811-chr2:99951417..99956311,9	MCF-7	breast:
14	chr2:99796217..99798600-chr2:100104908..100107681,3	K562	blood:
15	chr2:99796004..99796993-chr2:99952947..99953690,2	MCF-7	breast:
16	chr2:99796308..99800210-chr2:99949212..99956082,14	MCF-7	breast:

No data

Variant related genes	Relation type
C2orf15	TF binding region
MRPL30	TF binding region
MITD1	TF binding region
ENSG00000158417	Chromatin interaction
ENSG00000273155	Chromatin interaction
ENSG00000273045	Chromatin interaction
ENSG00000135945	Chromatin interaction
ENSG00000115514	Chromatin interaction
ENSG00000158411	Chromatin interaction
ENSG00000144182	Chromatin interaction
ENSG00000135951	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10496335	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123760	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11123767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1586434	0.86[EUR][1000 genomes]
rs17020569	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17022180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs17022249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28785294	1.00[EUR][1000 genomes]
rs28794804	0.83[ASN][1000 genomes]
rs35071324	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762472	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]
rs3791211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4850895	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs56926889	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57273701	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57743480	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58595226	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58635701	0.93[EUR][1000 genomes]
rs58745514	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59252741	0.82[ASN][1000 genomes]
rs59506582	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60056452	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60516303	0.83[ASN][1000 genomes]
rs60653099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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];0.87[ASN][1000 genomes]
rs7568749	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7608938	0.94[CHB][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	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' 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
rs10496334	LIPT1	cis	lymphoblastoid	seeQTL
rs10496334	LIPT1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99772400-99796800	Weak transcription	Colonic Mucosa	Colon
2	chr2:99772400-99797000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:99772600-99797000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:99784600-99797000	Weak transcription	Ovary	ovary
5	chr2:99785200-99797000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:99786600-99797000	Weak transcription	Aorta	Aorta
7	chr2:99786600-99797000	Weak transcription	Esophagus	oesophagus
8	chr2:99786600-99797000	Weak transcription	Lung	lung
9	chr2:99787600-99797000	Weak transcription	Psoas Muscle	Psoas
10	chr2:99792600-99797000	Weak transcription	Right Atrium	heart
11	chr2:99794600-99796800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:99794800-99796800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:99795000-99797000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr2:99795200-99796800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr2:99795200-99798400	Active TSS	GM12878-XiMat	blood
16	chr2:99795400-99796800	Enhancers	Brain Hippocampus Middle	brain
17	chr2:99795400-99796800	Enhancers	Brain Substantia Nigra	brain
18	chr2:99795400-99796800	Enhancers	Colon Smooth Muscle	Colon
19	chr2:99795400-99796800	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr2:99795400-99797000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:99795400-99797000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:99795400-99798800	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr2:99795600-99796800	Enhancers	Primary B cells from peripheral blood	blood
24	chr2:99795600-99796800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:99795600-99796800	Enhancers	Stomach Mucosa	stomach
26	chr2:99795600-99797000	Enhancers	Small Intestine	intestine
27	chr2:99795600-99799600	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr2:99795800-99796800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:99795800-99796800	Enhancers	Placenta	Placenta
30	chr2:99795800-99797000	Flanking Active TSS	Dnd41	blood
31	chr2:99795800-99798800	Active TSS	H1 Cell Line	embryonic stem cell
32	chr2:99795800-99799200	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr2:99796000-99796800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:99796000-99796800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:99796000-99796800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:99796000-99796800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr2:99796000-99797000	Weak transcription	Pancreas	Pancrea
38	chr2:99796000-99797200	Weak transcription	Gastric	stomach
39	chr2:99796000-99798600	Active TSS	Muscle Satellite Cultured Cells	--
40	chr2:99796000-99798800	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr2:99796000-99798800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:99796000-99799200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:99796200-99796800	Enhancers	Fetal Muscle Trunk	muscle
44	chr2:99796200-99796800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:99796200-99796800	Flanking Active TSS	HepG2	liver
46	chr2:99796200-99797000	Enhancers	Fetal Lung	lung
47	chr2:99796400-99796800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:99796400-99796800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:99796400-99796800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:99796400-99796800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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