Variant report

Variant	rs17086759
Chromosome Location	chr4:57282646-57282647
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57281906..57283505-chr4:57289215..57291492,2	MCF-7	breast:
2	chr4:57280047..57284869-chr4:57288459..57291870,6	K562	blood:
3	chr4:57275634..57278056-chr4:57281123..57283449,2	MCF-7	breast:
4	chr4:57273341..57278355-chr4:57278652..57283436,7	K562	blood:

Variant related genes	Relation type
ENSG00000268171	Chromatin interaction
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1140982	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1142851	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11934479	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11934636	1.00[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11940993	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12640212	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643989	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12643996	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12644498	1.00[CEU][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12649799	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12650288	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13102012	0.82[JPT][hapmap]
rs13124696	0.82[JPT][hapmap]
rs13134963	0.92[JPT][hapmap]
rs1579019	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17086773	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17086801	1.00[CEU][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17086804	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17086830	1.00[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17086838	1.00[CEU][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17086868	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17086898	0.87[EUR][1000 genomes]
rs17086909	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17086919	0.87[EUR][1000 genomes]
rs17086922	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2176785	0.92[JPT][hapmap]
rs2271924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34398021	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34419325	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35854625	0.82[ASN][1000 genomes]
rs3733324	0.94[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3733326	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796549	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796550	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4076103	1.00[CEU][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4128534	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs41498446	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs55778537	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55890437	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55903333	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909588	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56095772	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56129706	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56296497	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56362514	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56406704	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs57233429	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57245446	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58654038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59062367	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59153415	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59278715	0.86[ASN][1000 genomes]
rs59764923	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59828502	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6554347	0.82[JPT][hapmap]
rs6830145	1.00[CEU][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6831869	0.84[EUR][1000 genomes]
rs7437839	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7688482	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7694439	0.84[JPT][hapmap]

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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17086759	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
3	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:57272800-57292600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
7	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
8	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:57274000-57287000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr4:57274000-57290600	Weak transcription	GM12878-XiMat	blood
11	chr4:57274200-57287000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:57274200-57296400	Weak transcription	Dnd41	blood
13	chr4:57276800-57284200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:57277000-57287200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:57277000-57287200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:57277000-57287400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:57277000-57289800	Weak transcription	Fetal Stomach	stomach
18	chr4:57277000-57290000	Weak transcription	Aorta	Aorta
19	chr4:57277000-57290200	Weak transcription	Ovary	ovary
20	chr4:57277000-57290800	Weak transcription	Right Atrium	heart
21	chr4:57277000-57294200	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:57277000-57299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:57277000-57300000	Weak transcription	HSMM	muscle
24	chr4:57277200-57283000	Weak transcription	Fetal Intestine Small	intestine
25	chr4:57277800-57298000	Weak transcription	A549	lung
26	chr4:57278000-57286800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:57278000-57286800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:57278000-57290400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:57278000-57291600	Weak transcription	Brain Anterior Caudate	brain
30	chr4:57278000-57291600	Weak transcription	HepG2	liver
31	chr4:57278000-57294000	Weak transcription	HUVEC	blood vessel
32	chr4:57278000-57299200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:57278200-57283000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:57278200-57300200	Weak transcription	Fetal Kidney	kidney
35	chr4:57278200-57300200	Weak transcription	NHDF-Ad	bronchial
36	chr4:57278400-57290800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:57278600-57286800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:57278600-57287000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:57278600-57290600	Weak transcription	K562	blood
40	chr4:57278800-57283400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:57279400-57287200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr4:57280600-57291800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr4:57280600-57292600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr4:57280600-57297800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:57280800-57287000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:57280800-57299400	Weak transcription	Fetal Lung	lung
47	chr4:57281000-57282800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:57281000-57295000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:57281000-57299200	Weak transcription	HMEC	breast
50	chr4:57281600-57291600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links