Variant report

Variant	rs3748944
Chromosome Location	chr2:55750738-55750739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55749760..55752238-chr2:55760020..55761976,2	K562	blood:
2	chr2:55742826..55746774-chr2:55749245..55752700,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163001	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12618859	0.83[CHB][hapmap];0.93[MEX][hapmap]
rs12623937	0.84[CEU][hapmap];0.85[AMR][1000 genomes]
rs12987272	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12993839	0.92[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap]
rs12994656	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12998664	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs12998780	0.84[CHB][hapmap]
rs13001452	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13004436	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13007719	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13010217	0.84[CHB][hapmap]
rs13015243	0.82[AMR][1000 genomes]
rs13025331	0.84[CHB][hapmap]
rs13025994	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13030396	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17737233	0.84[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes]
rs1867334	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2054729	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2291336	0.94[MEX][hapmap]
rs34400247	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35057183	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35189503	0.87[AMR][1000 genomes]
rs35255044	0.82[AMR][1000 genomes]
rs35861320	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35968359	0.86[AMR][1000 genomes]
rs3748952	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3791654	0.83[CHB][hapmap]
rs3828238	0.93[MEX][hapmap]
rs6737995	0.84[CHB][hapmap];0.82[MEX][hapmap]
rs6753530	0.84[CEU][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55747600-55752200	Weak transcription	Lung	lung
2	chr2:55747600-55753000	Weak transcription	Spleen	Spleen
3	chr2:55747800-55751000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:55747800-55751200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:55747800-55751400	Weak transcription	Pancreas	Pancrea
6	chr2:55747800-55752000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:55747800-55752800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:55747800-55753600	Weak transcription	Gastric	stomach
9	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
10	chr2:55748000-55751400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:55748000-55751600	Weak transcription	Liver	Liver
12	chr2:55748000-55752000	Weak transcription	Stomach Mucosa	stomach
13	chr2:55748000-55752200	Weak transcription	Placenta	Placenta
14	chr2:55748000-55752200	Weak transcription	Ovary	ovary
15	chr2:55748000-55752200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:55748000-55752200	Weak transcription	Right Ventricle	heart
17	chr2:55748000-55752400	Weak transcription	Aorta	Aorta
18	chr2:55748000-55753000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:55748000-55757600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:55748000-55761200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:55748000-55761200	Weak transcription	Primary B cells from cord blood	blood
22	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
24	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
25	chr2:55748200-55750800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:55748200-55750800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:55748200-55750800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:55748200-55750800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:55748200-55750800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:55748200-55750800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:55748200-55750800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:55748200-55750800	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:55748200-55750800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:55748200-55750800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:55748200-55750800	Weak transcription	Fetal Thymus	thymus
36	chr2:55748200-55750800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:55748200-55750800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr2:55748200-55750800	Weak transcription	HSMM	muscle
39	chr2:55748200-55750800	Weak transcription	NHDF-Ad	bronchial
40	chr2:55748200-55751000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:55748200-55751000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:55748200-55751000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:55748200-55751000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:55748200-55751000	Weak transcription	Fetal Brain Female	brain
45	chr2:55748200-55751000	Weak transcription	Fetal Lung	lung
46	chr2:55748200-55751200	Weak transcription	Primary T cells from cord blood	blood
47	chr2:55748200-55751200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:55748200-55751200	Weak transcription	Brain Germinal Matrix	brain
49	chr2:55748200-55751200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr2:55748200-55751200	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links