Variant report

Variant	rs1386401
Chromosome Location	chr2:62889906-62889907
allele	C/G
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	EBF1	chr2:62889675-62889939	GM12878	blood:	n/a	n/a
2	EP300	chr2:62889516-62892400	SK-N-SH	brain:	n/a	chr2:62889587-62889601 chr2:62890249-62890258 chr2:62891356-62891370 chr2:62891753-62891767 chr2:62889967-62889976
3	TCF12	chr2:62889568-62891548	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM17-2	chr2:62889743-62889929	XLOC_002117
2	lnc-TMEM17-2	chr2:62889743-62889927	XLOC_002117
3	lnc-EHBP1-2	chr2:62889742-62889927	NONHSAT071024
4	lnc-TMEM17-2	chr2:62889743-62889929	XLOC_002117

Variant related genes	Relation type
ENSG00000226622	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10177638	0.80[ASN][1000 genomes]
rs10186082	0.82[EUR][1000 genomes]
rs10204410	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1038572	0.85[CEU][hapmap]
rs11125929	0.82[EUR][1000 genomes]
rs12328837	0.82[CEU][hapmap];0.82[CHB][hapmap];0.88[YRI][hapmap]
rs1386399	0.84[YRI][hapmap]
rs1406002	0.82[EUR][1000 genomes]
rs1487074	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs1534418	0.81[CEU][hapmap]
rs1534420	0.81[CEU][hapmap];0.83[YRI][hapmap]
rs1601673	0.82[EUR][1000 genomes]
rs1872790	0.82[CEU][hapmap];0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2204656	0.84[YRI][hapmap]
rs28798215	0.84[EUR][1000 genomes]
rs360799	0.87[YRI][hapmap]
rs62180020	0.83[EUR][1000 genomes]
rs6545961	0.82[EUR][1000 genomes]
rs6545962	0.83[EUR][1000 genomes]
rs6545963	0.83[EUR][1000 genomes]
rs6545969	0.88[CEU][hapmap];0.81[CHB][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6714927	0.80[AMR][1000 genomes]
rs6727888	0.82[AMR][1000 genomes]
rs6752597	0.83[EUR][1000 genomes]
rs6757128	0.88[CEU][hapmap];0.81[CHB][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7558681	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7578229	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7583570	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9989741	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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 miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv874232	chr2:62758044-62906084	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv834237	chr2:62762743-62926036	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62882000-62892000	Weak transcription	Fetal Intestine Large	intestine
2	chr2:62882400-62890000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:62886400-62890600	Enhancers	NHLF	lung
4	chr2:62886400-62893400	Enhancers	HMEC	breast
5	chr2:62886600-62892800	Enhancers	Osteobl	bone
6	chr2:62886600-62894000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:62886600-62894200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:62886800-62892200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:62887200-62894000	Enhancers	HepG2	liver
10	chr2:62887400-62894000	Enhancers	Colon Smooth Muscle	Colon
11	chr2:62887400-62899000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:62887600-62892000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:62887600-62893600	Enhancers	Rectal Smooth Muscle	rectum
14	chr2:62888000-62890800	Weak transcription	Fetal Heart	heart
15	chr2:62888000-62891600	Enhancers	Fetal Kidney	kidney
16	chr2:62888000-62893800	Enhancers	Fetal Lung	lung
17	chr2:62888200-62891800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:62888600-62890000	Enhancers	GM12878-XiMat	blood
19	chr2:62888600-62890200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:62888600-62890800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:62888600-62891800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr2:62888600-62892000	Weak transcription	Esophagus	oesophagus
23	chr2:62888600-62892400	Weak transcription	Pancreas	Pancrea
24	chr2:62888600-62893200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:62888600-62893200	Enhancers	NHEK	skin
26	chr2:62888800-62890200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:62888800-62890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:62888800-62891000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:62888800-62891000	Enhancers	NHDF-Ad	bronchial
30	chr2:62888800-62891400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:62888800-62891400	Weak transcription	Placenta	Placenta
32	chr2:62888800-62891800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:62888800-62892200	Enhancers	HSMM	muscle
34	chr2:62889000-62891000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:62889200-62891800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:62889200-62892200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:62889200-62892400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr2:62889400-62890000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:62889400-62890000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:62889400-62890000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:62889400-62891600	Enhancers	Brain Hippocampus Middle	brain
42	chr2:62889400-62892200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr2:62889400-62892200	Enhancers	HSMMtube	muscle
44	chr2:62889400-62893000	Enhancers	Adipose Nuclei	Adipose
45	chr2:62889600-62890000	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr2:62889600-62890000	Enhancers	H9 Cell Line	embryonic stem cell
47	chr2:62889600-62890000	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr2:62889600-62890000	Enhancers	Fetal Muscle Trunk	muscle
49	chr2:62889600-62890000	Flanking Active TSS	Ovary	ovary
50	chr2:62889600-62890000	Enhancers	Right Atrium	heart

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