Variant report

Variant	rs4369725
Chromosome Location	chr17:46006687-46006688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46005701..46007603-chr17:46012685..46014665,2	K562	blood:
2	chr17:46000022..46002269-chr17:46003613..46007289,3	MCF-7	breast:
3	chr17:46004717..46007682-chr17:46032533..46035119,2	K562	blood:
4	chr17:46005896..46008732-chr17:46011956..46013614,2	K562	blood:
5	chr17:46005203..46007396-chr17:46018097..46019833,3	MCF-7	breast:
6	chr17:45991270..45994231-chr17:46005074..46007219,2	K562	blood:
7	chr17:45989248..45990783-chr17:46005043..46007923,2	MCF-7	breast:
8	chr17:45972432..45975243-chr17:46004442..46007242,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108439	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10459927	0.84[ASN][1000 genomes]
rs11079801	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079803	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1108833	0.85[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs1130932	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652185	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11652827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654010	0.80[JPT][hapmap]
rs11655068	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11655352	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11659126	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870852	0.86[ASN][1000 genomes]
rs12601827	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12602494	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12939739	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13353189	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs2228251	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2228253	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2229358	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2318118	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2325747	0.89[ASN][1000 genomes]
rs2325751	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525107	0.81[ASN][1000 genomes]
rs3096	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs34593510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35280206	0.85[ASN][1000 genomes]
rs36124074	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764396	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4793731	0.85[ASN][1000 genomes]
rs4793732	0.81[ASN][1000 genomes]
rs4793733	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4793737	0.85[ASN][1000 genomes]
rs4794261	0.86[ASN][1000 genomes]
rs4794286	0.89[ASN][1000 genomes]
rs4794332	0.85[ASN][1000 genomes]
rs6503934	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67194241	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208707	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7211859	0.85[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs72840237	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8066893	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8071003	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895863	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903223	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS 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	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv2072	chr17:45998637-46019626	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4369725	SP2	Cis_1M	lymphoblastoid	RTeQTL
rs4369725	RP11-6N17.4	cis	Skin Sun Exposed Lower leg	GTEx
rs4369725	RP11-6N17.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
2	chr17:45992400-46008400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr17:45993800-46017400	Weak transcription	Psoas Muscle	Psoas
4	chr17:45994000-46013200	Weak transcription	Fetal Heart	heart
5	chr17:45995800-46012200	Weak transcription	HUVEC	blood vessel
6	chr17:45996000-46008200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr17:45996200-46008200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:45996200-46012600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:45996600-46008400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr17:45997400-46008200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr17:45998000-46008200	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr17:45998000-46009400	Strong transcription	Fetal Thymus	thymus
13	chr17:45998200-46008000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr17:45998200-46008200	Strong transcription	Dnd41	blood
15	chr17:45998200-46008400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr17:45998200-46008400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr17:45998200-46011000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr17:45998400-46008000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr17:45998400-46008200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr17:45998800-46008400	Strong transcription	Spleen	Spleen
21	chr17:45998800-46009600	Strong transcription	Placenta	Placenta
22	chr17:45999000-46008000	Strong transcription	Fetal Intestine Large	intestine
23	chr17:45999000-46008000	Strong transcription	Thymus	Thymus
24	chr17:45999000-46008200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr17:45999000-46008200	Strong transcription	Ovary	ovary
26	chr17:45999000-46008400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr17:45999000-46008400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr17:45999000-46008400	Strong transcription	Fetal Brain Female	brain
29	chr17:45999000-46009600	Strong transcription	Primary T cells from cord blood	blood
30	chr17:45999000-46010400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr17:45999200-46008200	Strong transcription	Primary B cells from cord blood	blood
32	chr17:45999200-46008400	Strong transcription	Brain Germinal Matrix	brain
33	chr17:45999200-46018200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr17:45999400-46007000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr17:45999400-46008000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr17:45999600-46010800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr17:45999800-46008400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:46000000-46007600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:46000000-46009000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr17:46000200-46007600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr17:46000200-46007800	Strong transcription	Colonic Mucosa	Colon
42	chr17:46000200-46008200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr17:46000400-46007200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr17:46000400-46007800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr17:46000400-46008000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr17:46000400-46008000	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr17:46000400-46008200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr17:46000600-46007000	Strong transcription	Osteobl	bone
49	chr17:46001000-46007000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr17:46001000-46010600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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