Variant report

Variant	rs4944893
Chromosome Location	chr11:74171280-74171281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:74170865..74173373-chr11:74203287..74204858,2	K562	blood:
2	chr11:74169758..74172325-chr11:74204191..74206118,2	K562	blood:
3	chr11:74169555..74172210-chr11:74251230..74253600,2	K562	blood:
4	chr11:74167420..74170050-chr11:74170321..74173103,2	MCF-7	breast:
5	chr11:74166040..74168250-chr11:74170163..74172017,2	K562	blood:
6	chr11:74169367..74173365-chr11:74176278..74179176,5	K562	blood:
7	chr11:74169876..74171653-chr11:74203244..74205851,2	MCF-7	breast:
8	chr11:74169160..74171524-chr11:74183873..74185733,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000254837	Chromatin interaction
ENSG00000175536	Chromatin interaction
ENSG00000175538	Chromatin interaction
ENSG00000077514	Chromatin interaction
ENSG00000254928	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11236118	0.83[YRI][hapmap]
rs11602340	0.85[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11602732	0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs12271302	0.83[YRI][hapmap]
rs12273068	0.83[YRI][hapmap]
rs12285733	0.83[YRI][hapmap]
rs12295841	0.83[YRI][hapmap]
rs603093	0.90[CHB][hapmap]
rs626930	0.91[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv555443	chr11:74109166-74180489	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1041154	chr11:74114801-74177909	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv393	chr11:74135862-74181417	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv832209	chr11:74155883-74329119	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4944893	LIPT2	cis	parietal	SCAN
rs4944893	PHOX2A	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74154800-74171600	Weak transcription	Fetal Kidney	kidney
2	chr11:74156600-74171400	Weak transcription	Psoas Muscle	Psoas
3	chr11:74160000-74173000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:74160400-74177800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:74160600-74173000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:74160800-74171400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:74161000-74171600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:74161000-74173000	Weak transcription	Brain Anterior Caudate	brain
9	chr11:74161400-74172800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:74166000-74172600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:74166800-74171400	Strong transcription	Fetal Intestine Small	intestine
12	chr11:74166800-74172800	Weak transcription	Left Ventricle	heart
13	chr11:74166800-74173000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:74167000-74172200	Weak transcription	Fetal Muscle Leg	muscle
15	chr11:74167400-74171600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr11:74167400-74171800	Strong transcription	Fetal Intestine Large	intestine
17	chr11:74167400-74175600	Strong transcription	Fetal Stomach	stomach
18	chr11:74167600-74172400	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:74168400-74171600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:74168600-74173200	Weak transcription	Spleen	Spleen
21	chr11:74168600-74175000	Weak transcription	Esophagus	oesophagus
22	chr11:74168600-74177600	Weak transcription	Small Intestine	intestine
23	chr11:74168800-74171600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr11:74169000-74174200	Weak transcription	Gastric	stomach
25	chr11:74169200-74172800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:74169400-74172400	Enhancers	Stomach Mucosa	stomach
27	chr11:74170000-74171400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:74170000-74172400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr11:74170400-74171600	Strong transcription	Fetal Lung	lung
30	chr11:74170400-74172000	Enhancers	Pancreas	Pancrea
31	chr11:74170600-74171400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:74170600-74171400	Flanking Active TSS	K562	blood
33	chr11:74170600-74172000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr11:74170600-74172400	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr11:74170600-74173600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr11:74170800-74171400	Enhancers	Colonic Mucosa	Colon
37	chr11:74170800-74171800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr11:74170800-74172200	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr11:74171000-74171400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
40	chr11:74171000-74171600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
41	chr11:74171000-74172200	Enhancers	Hela-S3	cervix
42	chr11:74171000-74173000	Enhancers	Liver	Liver
43	chr11:74171200-74171400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:74171200-74171400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr11:74171200-74171400	Enhancers	Lung	lung
46	chr11:74171200-74171600	Flanking Active TSS	Placenta	Placenta
47	chr11:74171200-74171600	Weak transcription	Ovary	ovary
48	chr11:74171200-74172200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:74171200-74172200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:74171200-74172200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum

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