Variant report

Variant	rs4664106
Chromosome Location	chr2:153242179-153242180
allele	A/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	NFIC	chr2:153242158-153242718	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr2:153241991-153244319	SK-N-SH	brain:	n/a	chr2:153242638-153242652 chr2:153243952-153243960 chr2:153242319-153242329

Variant related genes	Relation type
ENSG00000213197	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10432492	0.91[MEX][hapmap]
rs10931069	0.80[MEX][hapmap]
rs11674872	0.83[GIH][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes]
rs12466536	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12478426	0.91[MEX][hapmap]
rs13405341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13418521	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16831013	0.87[JPT][hapmap]
rs16831028	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2345873	0.84[CHD][hapmap];0.90[MEX][hapmap]
rs2345903	0.80[MEX][hapmap]
rs36039059	0.87[AMR][1000 genomes]
rs3762622	0.86[JPT][hapmap]
rs3890370	0.84[CHD][hapmap];0.90[MEX][hapmap]
rs4528717	0.82[CHD][hapmap]
rs4664103	0.80[MEX][hapmap]
rs59388039	0.80[AMR][1000 genomes]
rs6715843	0.80[MEX][hapmap]
rs6737699	0.83[CHD][hapmap]
rs6761815	0.85[JPT][hapmap]
rs7586834	0.81[GIH][hapmap]
rs7593505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7600624	0.81[GIH][hapmap]
rs9677380	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][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	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1005012	chr2:153206764-153273886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153207600-153246400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:153224800-153246000	Weak transcription	Fetal Stomach	stomach
3	chr2:153226200-153249400	Weak transcription	Right Ventricle	heart
4	chr2:153226200-153251800	Weak transcription	HSMMtube	muscle
5	chr2:153229200-153252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:153233200-153242200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:153233400-153249000	Weak transcription	Gastric	stomach
8	chr2:153233600-153246200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:153233800-153245600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:153233800-153255400	Weak transcription	NHEK	skin
11	chr2:153235400-153243200	Weak transcription	Stomach Mucosa	stomach
12	chr2:153237400-153246200	Weak transcription	Placenta	Placenta
13	chr2:153237400-153249000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:153237400-153255400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:153237400-153255400	Weak transcription	HMEC	breast
16	chr2:153238400-153242400	Weak transcription	Fetal Brain Female	brain
17	chr2:153238400-153246400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:153238600-153243400	Weak transcription	Fetal Lung	lung
19	chr2:153238600-153245600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:153238600-153246600	Weak transcription	Ovary	ovary
21	chr2:153238600-153258600	Weak transcription	Left Ventricle	heart
22	chr2:153238800-153242200	Weak transcription	Fetal Kidney	kidney
23	chr2:153239000-153242600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:153239200-153243400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:153239400-153242200	Enhancers	NHDF-Ad	bronchial
26	chr2:153239400-153242600	Enhancers	Brain Angular Gyrus	brain
27	chr2:153239600-153242400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:153240000-153242600	Enhancers	Fetal Muscle Leg	muscle
29	chr2:153240200-153243400	Enhancers	HepG2	liver
30	chr2:153240600-153243000	Enhancers	Brain Anterior Caudate	brain
31	chr2:153240600-153243600	Enhancers	Brain Hippocampus Middle	brain
32	chr2:153240600-153244400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr2:153240800-153242800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:153240800-153242800	Enhancers	Psoas Muscle	Psoas
35	chr2:153240800-153242800	Enhancers	A549	lung
36	chr2:153240800-153243600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:153240800-153243600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:153240800-153243800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:153240800-153244000	Enhancers	Brain Substantia Nigra	brain
40	chr2:153241000-153242200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:153241200-153242600	Weak transcription	NHLF	lung
42	chr2:153241200-153244200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:153241200-153245600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:153241200-153251600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:153241200-153255400	Weak transcription	Pancreas	Pancrea
46	chr2:153241600-153242800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr2:153241600-153243000	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr2:153241600-153243000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:153241600-153243000	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr2:153241600-153243400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links