Variant report

Variant	rs3805601
Chromosome Location	chr5:108085743-108085744
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:108060235..108074407-chr5:108078172..108087811,48	K562	blood:
2	chr5:108084910..108087021-chr5:108747518..108750406,2	K562	blood:
3	chr5:108062273..108066431-chr5:108081834..108086243,5	MCF-7	breast:
4	chr5:108059312..108068052-chr5:108079113..108087366,42	K562	blood:

Variant related genes	Relation type
ENSG00000272523	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10036583	1.00[JPT][hapmap]
rs10037675	1.00[JPT][hapmap]
rs10039132	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10039951	1.00[JPT][hapmap]
rs10041657	1.00[JPT][hapmap]
rs10042152	1.00[JPT][hapmap]
rs10042569	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10050547	1.00[JPT][hapmap]
rs10052208	1.00[JPT][hapmap]
rs10052531	1.00[JPT][hapmap]
rs10054086	1.00[JPT][hapmap]
rs10061811	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10064960	1.00[JPT][hapmap]
rs10065605	1.00[JPT][hapmap]
rs10065611	1.00[JPT][hapmap]
rs10066173	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10070327	1.00[JPT][hapmap]
rs10077917	1.00[JPT][hapmap]
rs10214241	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10223256	0.82[JPT][hapmap]
rs10477428	1.00[JPT][hapmap]
rs10477429	1.00[JPT][hapmap]
rs10477432	1.00[JPT][hapmap]
rs10477931	1.00[JPT][hapmap]
rs11741855	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11748534	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12719099	1.00[JPT][hapmap]
rs13358881	1.00[JPT][hapmap]
rs13359423	1.00[JPT][hapmap]
rs13360253	1.00[JPT][hapmap]
rs1396444	1.00[JPT][hapmap]
rs1423456	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423459	1.00[JPT][hapmap]
rs17161463	0.92[ASN][1000 genomes]
rs17161466	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17161476	0.82[TSI][hapmap]
rs17161505	1.00[JPT][hapmap]
rs17161540	1.00[JPT][hapmap]
rs17161562	1.00[JPT][hapmap]
rs17163941	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2009646	1.00[JPT][hapmap]
rs2081128	1.00[JPT][hapmap]
rs2113001	1.00[JPT][hapmap]
rs2229085	1.00[JPT][hapmap]
rs28376017	0.92[ASN][1000 genomes]
rs2900037	1.00[JPT][hapmap]
rs35141056	1.00[JPT][hapmap]
rs3805600	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3828655	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41508849	1.00[JPT][hapmap]
rs4358573	1.00[JPT][hapmap]
rs4361568	1.00[JPT][hapmap]
rs4479887	1.00[JPT][hapmap]
rs4560594	1.00[JPT][hapmap]
rs4560595	1.00[JPT][hapmap]
rs62361298	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62361300	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6594341	1.00[JPT][hapmap]
rs6859105	0.80[ASN][1000 genomes]
rs6859750	0.80[ASN][1000 genomes]
rs6869591	0.93[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6870408	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6873130	1.00[JPT][hapmap]
rs6873917	1.00[JPT][hapmap]
rs6888173	1.00[JPT][hapmap]
rs7711892	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7715658	1.00[JPT][hapmap]
rs7716320	0.82[TSI][hapmap]
rs7728920	1.00[JPT][hapmap]
rs889269	1.00[JPT][hapmap]
rs9326750	1.00[JPT][hapmap]
rs9326752	1.00[JPT][hapmap]
rs9885265	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108082600-108085800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:108082600-108085800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:108082600-108085800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:108082600-108086000	Active TSS	GM12878-XiMat	blood
5	chr5:108082600-108086200	Active TSS	Right Atrium	heart
6	chr5:108082600-108087000	Active TSS	Stomach Smooth Muscle	stomach
7	chr5:108082800-108085800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr5:108082800-108085800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:108082800-108085800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:108082800-108086000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr5:108082800-108086200	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr5:108082800-108086200	Active TSS	NHLF	lung
13	chr5:108082800-108086400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:108082800-108086400	Active TSS	NHDF-Ad	bronchial
15	chr5:108083000-108085800	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr5:108083000-108085800	Active TSS	Colon Smooth Muscle	Colon
17	chr5:108083000-108085800	Active TSS	Fetal Intestine Large	intestine
18	chr5:108083000-108085800	Active TSS	Psoas Muscle	Psoas
19	chr5:108083000-108085800	Active TSS	HSMMtube	muscle
20	chr5:108083000-108086000	Active TSS	NHEK	skin
21	chr5:108083200-108085800	Active TSS	Fetal Intestine Small	intestine
22	chr5:108083200-108085800	Active TSS	Fetal Muscle Leg	muscle
23	chr5:108083200-108085800	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr5:108083200-108086000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:108083200-108086200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:108083200-108086200	Active TSS	Fetal Brain Female	brain
27	chr5:108083200-108086200	Active TSS	HMEC	breast
28	chr5:108083400-108085800	Active TSS	H9 Cell Line	embryonic stem cell
29	chr5:108083400-108085800	Active TSS	A549	lung
30	chr5:108083400-108085800	Active TSS	HSMM	muscle
31	chr5:108083600-108085800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:108083600-108085800	Active TSS	Rectal Smooth Muscle	rectum
33	chr5:108083800-108086200	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr5:108083800-108086200	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr5:108084600-108085800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:108084800-108085800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr5:108085000-108085800	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr5:108085000-108085800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:108085000-108085800	Flanking Active TSS	Fetal Brain Male	brain
40	chr5:108085200-108085800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:108085200-108085800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:108085200-108085800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr5:108085200-108085800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:108085200-108085800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:108085200-108085800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr5:108085200-108085800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:108085200-108085800	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr5:108085200-108085800	Active TSS	Brain Germinal Matrix	brain
49	chr5:108085200-108085800	Flanking Active TSS	Fetal Lung	lung
50	chr5:108085200-108085800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links