Variant report

Variant	rs225308
Chromosome Location	chr17:33917190-33917191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:33903370..33909494-chr17:33910892..33920548,27	MCF-7	breast:
2	chr17:33865496..33867936-chr17:33913565..33917669,3	K562	blood:
3	chr17:33916904..33919216-chr17:33993404..33995883,2	K562	blood:

Variant related genes	Relation type
ENSG00000108733	Chromatin interaction
ENSG00000267035	Chromatin interaction
ENSG00000006125	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10438814	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1080352	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11080356	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11652234	1.00[ASN][1000 genomes]
rs1634683	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17550632	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17550716	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17638867	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs178736	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188959	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2011528	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2011897	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225244	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225246	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225248	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225249	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225250	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225252	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225256	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225257	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225258	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225260	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225261	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225264	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225265	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225266	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225267	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225268	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225270	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225271	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225274	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225275	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225276	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225278	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225279	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225283	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225285	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs225286	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225287	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225288	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225292	0.88[EUR][1000 genomes]
rs225294	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225296	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225298	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225300	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225305	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225307	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226084	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226087	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226089	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226090	0.94[EUR][1000 genomes]
rs2376177	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428464	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2523114	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2523116	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2523117	0.84[EUR][1000 genomes]
rs2626625	0.94[EUR][1000 genomes]
rs2626626	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35542792	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3859282	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3859284	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3890900	0.89[EUR][1000 genomes]
rs4795086	0.91[EUR][1000 genomes]
rs4796098	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4796100	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796101	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796104	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6505484	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505485	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505486	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505487	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7208672	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7210966	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7211724	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7213804	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7214250	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7214742	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7217378	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7217533	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7221203	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72828038	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72829922	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829923	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829925	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829927	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829932	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829933	0.84[EUR][1000 genomes]
rs7405825	0.91[ASN][1000 genomes]
rs8064895	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8071584	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8072676	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8074800	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8077826	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9303690	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9649	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9912939	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription 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 Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs225308	LOC645744	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33914000-33918200	Active TSS	K562	blood
2	chr17:33915000-33922000	Weak transcription	Spleen	Spleen
3	chr17:33915000-33923600	Weak transcription	Gastric	stomach
4	chr17:33915200-33918000	Weak transcription	Lung	lung
5	chr17:33915200-33918200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:33915200-33921800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr17:33915200-33923400	Weak transcription	Colonic Mucosa	Colon
8	chr17:33915200-33923600	Weak transcription	Esophagus	oesophagus
9	chr17:33915200-33923600	Weak transcription	Pancreas	Pancrea
10	chr17:33915200-33930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:33915200-33932600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:33915400-33923600	Weak transcription	Aorta	Aorta
13	chr17:33915600-33917400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr17:33915600-33919400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr17:33915600-33920600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr17:33915600-33920800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:33915600-33921000	Weak transcription	Placenta	Placenta
18	chr17:33915600-33921200	Weak transcription	Fetal Thymus	thymus
19	chr17:33915600-33921800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr17:33915600-33922200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:33915600-33923600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:33915600-33954600	Weak transcription	Small Intestine	intestine
23	chr17:33915800-33918000	Weak transcription	Left Ventricle	heart
24	chr17:33915800-33918200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr17:33915800-33918400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr17:33915800-33921000	Weak transcription	HSMMtube	muscle
27	chr17:33915800-33921200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr17:33915800-33921800	Weak transcription	Thymus	Thymus
29	chr17:33915800-33922000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr17:33915800-33922000	Weak transcription	Fetal Muscle Leg	muscle
31	chr17:33915800-33923600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr17:33915800-33923600	Weak transcription	Right Ventricle	heart
33	chr17:33916000-33917400	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr17:33916000-33917800	Enhancers	Brain Cingulate Gyrus	brain
35	chr17:33916000-33917800	Enhancers	Fetal Brain Female	brain
36	chr17:33916000-33918200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr17:33916000-33920600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr17:33916000-33920600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr17:33916000-33921800	Weak transcription	Psoas Muscle	Psoas
40	chr17:33916000-33923800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr17:33916000-33942000	Weak transcription	Right Atrium	heart
42	chr17:33916400-33918000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr17:33916400-33920800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr17:33916400-33924200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr17:33916400-33944800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr17:33916600-33917400	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr17:33916600-33918200	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr17:33916600-33918800	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr17:33916600-33920600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr17:33916600-33920800	Weak transcription	Primary B cells from cord blood	blood

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