Variant report

Variant	rs9903223
Chromosome Location	chr17:46008257-46008258
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46007432..46009811-chr17:46047388..46051059,3	K562	blood:
2	chr17:45974031..45975859-chr17:46008200..46010414,2	MCF-7	breast:
3	chr17:46003485..46006244-chr17:46007523..46010248,2	K562	blood:
4	chr17:45992911..45994770-chr17:46006904..46009157,2	K562	blood:
5	chr17:46005896..46008732-chr17:46011956..46013614,2	K562	blood:
6	chr17:46007857..46010307-chr17:46016278..46019958,3	K562	blood:
7	chr17:46008254..46011151-chr17:46023044..46026189,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108439	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000264019	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10459927	0.84[ASN][1000 genomes]
rs11079801	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079803	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1108833	0.86[ASN][1000 genomes]
rs1130932	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652185	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11652827	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655068	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11655352	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11659126	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870852	0.86[ASN][1000 genomes]
rs12601827	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12602494	0.85[ASN][1000 genomes]
rs12939739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228251	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2228253	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2229358	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2318118	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2325747	0.89[ASN][1000 genomes]
rs2325751	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525107	0.81[ASN][1000 genomes]
rs3096	0.85[ASN][1000 genomes]
rs34593510	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35280206	0.85[ASN][1000 genomes]
rs36124074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764396	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4369725	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793731	0.85[ASN][1000 genomes]
rs4793732	0.81[ASN][1000 genomes]
rs4793733	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	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67194241	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208707	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7211859	0.86[ASN][1000 genomes]
rs72840237	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8066893	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8071003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895863	1.00[AFR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9903223	SP2	Cis_1M	lymphoblastoid	RTeQTL
rs9903223	RP11-6N17.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:120 , 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	chr17:45996200-46012600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr17:45996600-46008400	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr17:45998000-46009400	Strong transcription	Fetal Thymus	thymus
9	chr17:45998200-46008400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr17:45998200-46008400	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr17:45998200-46011000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr17:45998800-46008400	Strong transcription	Spleen	Spleen
13	chr17:45998800-46009600	Strong transcription	Placenta	Placenta
14	chr17:45999000-46008400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr17:45999000-46008400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:45999000-46008400	Strong transcription	Fetal Brain Female	brain
17	chr17:45999000-46009600	Strong transcription	Primary T cells from cord blood	blood
18	chr17:45999000-46010400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr17:45999200-46008400	Strong transcription	Brain Germinal Matrix	brain
20	chr17:45999200-46018200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr17:45999600-46010800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:45999800-46008400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:46000000-46009000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr17:46001000-46010600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr17:46002400-46013400	Weak transcription	Stomach Mucosa	stomach
26	chr17:46003000-46008600	Strong transcription	Lung	lung
27	chr17:46003000-46012200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr17:46003200-46009000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr17:46003200-46009200	Weak transcription	Fetal Kidney	kidney
30	chr17:46003200-46009400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr17:46003200-46012000	Weak transcription	HMEC	breast
32	chr17:46003200-46012000	Weak transcription	NHDF-Ad	bronchial
33	chr17:46003200-46012200	Weak transcription	NH-A	brain
34	chr17:46003200-46012200	Weak transcription	NHEK	skin
35	chr17:46003200-46014200	Weak transcription	GM12878-XiMat	blood
36	chr17:46003200-46018400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr17:46004400-46012600	Weak transcription	Hela-S3	cervix
38	chr17:46004600-46008800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr17:46004600-46013200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr17:46004600-46018200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr17:46005400-46012400	Weak transcription	NHLF	lung
42	chr17:46005400-46017400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr17:46005400-46018200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr17:46005600-46009200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr17:46006000-46008400	Strong transcription	Fetal Lung	lung
46	chr17:46006200-46008400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr17:46006200-46017800	Weak transcription	Small Intestine	intestine
48	chr17:46006400-46008400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr17:46006400-46008400	Genic enhancers	Right Ventricle	heart
50	chr17:46006600-46011200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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