Variant report

Variant	rs4835948
Chromosome Location	chr5:127870190-127870191
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	NFIC	chr5:127870141-127870955	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
SLC27A6	TF binding region

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

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

rs_ID	r²[population]
rs10040225	0.89[JPT][hapmap]
rs10066170	0.81[AFR][1000 genomes]
rs10463844	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1092414	0.80[ASN][1000 genomes]
rs11241957	0.89[JPT][hapmap]
rs11241959	0.83[JPT][hapmap]
rs12656510	0.80[JPT][hapmap]
rs12658318	0.90[JPT][hapmap]
rs1435514	0.89[JPT][hapmap]
rs17677603	0.84[CEU][hapmap];0.89[JPT][hapmap]
rs1858079	0.89[JPT][hapmap]
rs1897999	0.81[AFR][1000 genomes]
rs2263510	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2409539	0.89[JPT][hapmap]
rs331078	0.83[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs331083	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs331087	0.80[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3805647	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4145849	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs4836373	0.83[JPT][hapmap]
rs62390667	0.81[AFR][1000 genomes]
rs6595828	0.89[JPT][hapmap]
rs6859216	0.89[JPT][hapmap]
rs6892983	0.89[JPT][hapmap]
rs764368	0.89[JPT][hapmap]
rs7719223	0.89[JPT][hapmap]
rs7721622	0.83[JPT][hapmap]
rs7726680	0.89[JPT][hapmap]
rs7734008	0.89[JPT][hapmap]
rs813308	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv2763497	chr5:127745955-127882468	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv530822	chr5:127777365-127900742	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv427734	chr5:127805281-128088632	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1019560	chr5:127814656-127873680	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv537895	chr5:127814656-127873680	ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127827200-127870400	Weak transcription	Fetal Kidney	kidney
2	chr5:127840200-127870400	Weak transcription	Left Ventricle	heart
3	chr5:127840200-127872000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:127841000-127870200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:127845600-127870400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:127853200-127872400	Weak transcription	Osteobl	bone
7	chr5:127854000-127872000	Weak transcription	Ovary	ovary
8	chr5:127855000-127871200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:127860200-127870400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:127861000-127870600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:127861000-127871000	Weak transcription	A549	lung
12	chr5:127861000-127871800	Weak transcription	Fetal Lung	lung
13	chr5:127862600-127872000	Weak transcription	NHLF	lung
14	chr5:127863200-127872000	Weak transcription	HUVEC	blood vessel
15	chr5:127863600-127872000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:127864600-127871800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:127866200-127870600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr5:127866400-127870400	Weak transcription	NH-A	brain
19	chr5:127866400-127871000	Weak transcription	HMEC	breast
20	chr5:127866600-127870600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:127867200-127871800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:127867800-127870400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:127868200-127870400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:127868200-127870600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:127868400-127870600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:127868400-127871800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr5:127868600-127870600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:127868600-127871800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:127868800-127871800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:127869000-127870400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:127869000-127870600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:127869200-127870200	Weak transcription	NHEK	skin
33	chr5:127869200-127870400	Weak transcription	NHDF-Ad	bronchial
34	chr5:127869200-127871600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:127869200-127871800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr5:127869200-127871800	Weak transcription	Right Ventricle	heart
37	chr5:127869200-127872000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:127869200-127875000	Active TSS	Fetal Heart	heart
39	chr5:127869400-127870400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr5:127869400-127870400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:127869400-127870400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:127869400-127870400	Weak transcription	Fetal Muscle Leg	muscle
43	chr5:127869400-127870400	Weak transcription	Placenta	Placenta
44	chr5:127869400-127870400	Weak transcription	Fetal Stomach	stomach
45	chr5:127869600-127870400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:127870000-127870200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:127870000-127871000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links