Variant report

Variant	rs3814005
Chromosome Location	chr1:47899897-47899898
allele	C/T
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	chr1:47899546-47900621	H1-neurons	neurons:	n/a	n/a
2	BHLHE40	chr1:47899734-47899934	GM12878	blood:	n/a	n/a
3	SUZ12	chr1:47898147-47900955	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr1:47899608-47900481	H1-hESC	embryonic stem cell:	n/a	n/a
5	CHD2	chr1:47899789-47899931	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:47899572-47900515	H1-neurons	neurons:	n/a	n/a
7	CHD1	chr1:47899810-47899987	GM12878	blood:	n/a	n/a
8	CTBP2	chr1:47899428-47900976	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STIL-2	chr1:47897805-47900313	ENSG00000237424.1
2	lnc-STIL-2	chr1:47897807-47900313	NR_026878

Variant related genes	Relation type
FOXD2	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10789508	0.88[AMR][1000 genomes]
rs10890481	0.84[ASN][1000 genomes]
rs12031011	0.88[EUR][1000 genomes]
rs12035995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036198	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12046016	0.94[AMR][1000 genomes]
rs12404237	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17103251	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17103253	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4600090	0.83[GIH][hapmap]
rs4926858	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4926865	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4926870	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926871	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6665045	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6666370	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs6673789	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6674100	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6689636	0.88[AMR][1000 genomes]
rs6690084	0.83[GIH][hapmap]
rs6697911	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72902514	0.88[AMR][1000 genomes]
rs870357	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534956	chr1:47882277-47905486	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv534957	chr1:47882277-47907965	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr1:47894400-47901600	Weak transcription	HepG2	liver
2	chr1:47896800-47900600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr1:47897000-47900200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:47897000-47901600	Weak transcription	A549	lung
5	chr1:47897200-47900400	Enhancers	Liver	Liver
6	chr1:47897200-47900600	Bivalent Enhancer	Fetal Stomach	stomach
7	chr1:47897600-47900200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr1:47897600-47900400	Bivalent Enhancer	Fetal Thymus	thymus
9	chr1:47897800-47900200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:47897800-47900400	Bivalent Enhancer	Fetal Heart	heart
11	chr1:47898000-47900000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
12	chr1:47898000-47900200	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr1:47898000-47900400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
14	chr1:47898000-47900400	Flanking Active TSS	HMEC	breast
15	chr1:47898000-47900600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:47898200-47900400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:47898200-47901000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:47898400-47900400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:47898400-47900400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:47898400-47900400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:47898400-47900400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:47898400-47900800	Bivalent Enhancer	Esophagus	oesophagus
23	chr1:47898600-47900000	Bivalent Enhancer	Fetal Lung	lung
24	chr1:47898600-47900200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:47898600-47900200	Weak transcription	NHLF	lung
26	chr1:47898600-47900400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr1:47898600-47900400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:47898600-47900600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
29	chr1:47898600-47900600	Bivalent Enhancer	Fetal Brain Male	brain
30	chr1:47898600-47900800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:47898600-47900800	Bivalent Enhancer	Placenta	Placenta
32	chr1:47898600-47901200	Weak transcription	Hela-S3	cervix
33	chr1:47898800-47900000	Bivalent Enhancer	Stomach Mucosa	stomach
34	chr1:47898800-47900200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
35	chr1:47898800-47900400	Enhancers	Lung	lung
36	chr1:47898800-47900400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
37	chr1:47898800-47900400	Bivalent Enhancer	Spleen	Spleen
38	chr1:47898800-47900600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
39	chr1:47898800-47901400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:47898800-47901600	Weak transcription	K562	blood
41	chr1:47898800-47902000	Weak transcription	HSMM	muscle
42	chr1:47898800-47902000	Weak transcription	HSMMtube	muscle
43	chr1:47899000-47900200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
44	chr1:47899000-47900200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
45	chr1:47899000-47900400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr1:47899000-47901200	Genic enhancers	Dnd41	blood
47	chr1:47899000-47901400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:47899000-47904400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
49	chr1:47899200-47900000	Weak transcription	Aorta	Aorta
50	chr1:47899200-47900000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain

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