Variant report

Variant	rs12948669
Chromosome Location	chr17:33918076-33918077
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	chr17:33867300..33869220-chr17:33917248..33919262,2	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: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1037590	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1037592	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10512472	0.83[AMR][1000 genomes]
rs11653357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655803	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11656138	0.84[ASN][1000 genomes]
rs11868206	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12604067	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12947592	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1671656	0.83[ASN][1000 genomes]
rs16971217	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16971227	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1968578	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs225243	0.83[ASN][1000 genomes]
rs225247	0.83[ASN][1000 genomes]
rs225251	0.83[ASN][1000 genomes]
rs225254	0.83[ASN][1000 genomes]
rs225259	0.80[ASN][1000 genomes]
rs225262	0.81[ASN][1000 genomes]
rs225277	0.81[ASN][1000 genomes]
rs225295	0.84[ASN][1000 genomes]
rs225304	0.84[ASN][1000 genomes]
rs225306	0.83[ASN][1000 genomes]
rs2889311	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35237539	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213476	0.90[ASN][1000 genomes]
rs7503168	0.81[AMR][1000 genomes]
rs9890191	0.96[ASN][1000 genomes]
rs9891574	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9897552	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9899860	0.98[ASN][1000 genomes]
rs9899927	0.98[ASN][1000 genomes]
rs9900378	0.84[ASN][1000 genomes]
rs9902765	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9907772	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9913875	0.98[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

No data

Chromatin state (count:125 , 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	chr17:33915200-33918200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr17:33915200-33921800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr17:33915200-33923400	Weak transcription	Colonic Mucosa	Colon
7	chr17:33915200-33923600	Weak transcription	Esophagus	oesophagus
8	chr17:33915200-33923600	Weak transcription	Pancreas	Pancrea
9	chr17:33915200-33930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:33915200-33932600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr17:33915400-33923600	Weak transcription	Aorta	Aorta
12	chr17:33915600-33919400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:33915600-33920600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr17:33915600-33920800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:33915600-33921000	Weak transcription	Placenta	Placenta
16	chr17:33915600-33921200	Weak transcription	Fetal Thymus	thymus
17	chr17:33915600-33921800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr17:33915600-33922200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr17:33915600-33923600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:33915600-33954600	Weak transcription	Small Intestine	intestine
21	chr17:33915800-33918200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:33915800-33918400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr17:33915800-33921000	Weak transcription	HSMMtube	muscle
24	chr17:33915800-33921200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr17:33915800-33921800	Weak transcription	Thymus	Thymus
26	chr17:33915800-33922000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr17:33915800-33922000	Weak transcription	Fetal Muscle Leg	muscle
28	chr17:33915800-33923600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr17:33915800-33923600	Weak transcription	Right Ventricle	heart
30	chr17:33916000-33918200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:33916000-33920600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr17:33916000-33920600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr17:33916000-33921800	Weak transcription	Psoas Muscle	Psoas
34	chr17:33916000-33923800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr17:33916000-33942000	Weak transcription	Right Atrium	heart
36	chr17:33916400-33920800	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr17:33916400-33924200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr17:33916400-33944800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr17:33916600-33918200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr17:33916600-33918800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr17:33916600-33920600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr17:33916600-33920800	Weak transcription	Primary B cells from cord blood	blood
43	chr17:33916600-33920800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:33916600-33921200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr17:33916600-33921200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr17:33916600-33921600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr17:33916600-33921600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr17:33916600-33922000	Weak transcription	Brain Hippocampus Middle	brain
49	chr17:33916600-33923800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr17:33916800-33918400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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