Variant report

Variant	rs877975
Chromosome Location	chr15:52966227-52966228
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52965949..52968646-chr15:53025332..53028243,3	MCF-7	breast:
2	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:
3	chr15:52966022..52968187-chr15:52971881..52974523,2	K562	blood:
4	chr15:52964942..52967730-chr15:52969807..52971860,2	K562	blood:

Variant related genes	Relation type
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs17651844	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap]
rs17651850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17708373	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2414172	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35689765	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57141956	0.85[EUR][1000 genomes]
rs59336405	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59360599	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59808396	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59920981	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59997215	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60200908	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61021982	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7182896	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72623993	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72623994	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72623995	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72623996	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72623997	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72623998	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72623999	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72624000	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs877974	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs933861	0.98[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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv457140	chr15:52901433-52968746	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr15:52944400-52969600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:52944400-52970200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:52944600-52969800	Weak transcription	Fetal Brain Male	brain
5	chr15:52945000-52968600	Weak transcription	HepG2	liver
6	chr15:52946000-52968200	Weak transcription	Fetal Heart	heart
7	chr15:52946000-52968600	Weak transcription	Stomach Mucosa	stomach
8	chr15:52949400-52966400	Strong transcription	Duodenum Mucosa	Duodenum
9	chr15:52950400-52969400	Weak transcription	A549	lung
10	chr15:52950800-52968400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:52951000-52970200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:52952000-52967400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr15:52952000-52968000	Strong transcription	Fetal Thymus	thymus
14	chr15:52952200-52967800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr15:52953200-52967800	Weak transcription	Fetal Intestine Small	intestine
16	chr15:52957000-52966400	Weak transcription	Esophagus	oesophagus
17	chr15:52957400-52967400	Weak transcription	Right Atrium	heart
18	chr15:52957400-52970000	Weak transcription	Colonic Mucosa	Colon
19	chr15:52957400-52970000	Weak transcription	Lung	lung
20	chr15:52958000-52966800	Strong transcription	NHDF-Ad	bronchial
21	chr15:52958200-52966400	Strong transcription	Liver	Liver
22	chr15:52959200-52967200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:52960000-52969000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:52960400-52967600	Weak transcription	Ovary	ovary
25	chr15:52960400-52969600	Weak transcription	HMEC	breast
26	chr15:52960600-52969400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:52960600-52969400	Weak transcription	NHEK	skin
28	chr15:52960600-52970000	Weak transcription	Small Intestine	intestine
29	chr15:52961600-52966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:52961600-52969000	Strong transcription	Osteobl	bone
31	chr15:52962000-52967600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:52962200-52967800	Strong transcription	Fetal Lung	lung
33	chr15:52962200-52967800	Strong transcription	NH-A	brain
34	chr15:52962200-52969800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr15:52962400-52969400	Weak transcription	Fetal Stomach	stomach
36	chr15:52962600-52966800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:52962600-52967800	Weak transcription	Pancreas	Pancrea
38	chr15:52962600-52968600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr15:52962600-52969800	Weak transcription	Right Ventricle	heart
40	chr15:52962600-52970200	Weak transcription	Gastric	stomach
41	chr15:52962600-52970400	Weak transcription	Spleen	Spleen
42	chr15:52962800-52969400	Weak transcription	Aorta	Aorta
43	chr15:52963000-52966800	Strong transcription	Fetal Intestine Large	intestine
44	chr15:52963000-52969600	Weak transcription	NHLF	lung
45	chr15:52963000-52970000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:52963200-52967400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr15:52963600-52968800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr15:52963800-52967200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr15:52964000-52969000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr15:52964200-52968600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links