Variant report

Variant	rs16964486
Chromosome Location	chr15:52011490-52011491
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52010154..52013648-chr15:52016687..52020314,4	MCF-7	breast:
2	chr15:52008451..52011571-chr15:52027342..52031770,5	MCF-7	breast:
3	chr15:51970627..51972181-chr15:52008855..52011853,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1350173	0.83[EUR][1000 genomes]
rs16953082	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs16964488	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs16964505	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16964506	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16964507	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs16964508	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16964510	0.95[EUR][1000 genomes]
rs16964518	0.95[EUR][1000 genomes]
rs16964528	0.83[EUR][1000 genomes]
rs16964532	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs16964555	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs16964561	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs16964579	0.85[EUR][1000 genomes]
rs16964585	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs16964596	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs17705373	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17705685	1.00[YRI][hapmap]
rs1991267	1.00[JPT][hapmap]
rs2414115	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2570232	1.00[CEU][hapmap]
rs2593181	1.00[JPT][hapmap]
rs2899478	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3751595	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794529	0.88[EUR][1000 genomes]
rs3794533	1.00[YRI][hapmap]
rs4499184	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4775971	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs56221158	0.93[EUR][1000 genomes]
rs60398357	0.83[EUR][1000 genomes]
rs7164550	1.00[MEX][hapmap]
rs7165594	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166954	0.91[EUR][1000 genomes]
rs7167759	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168775	1.00[YRI][hapmap]
rs7174616	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7175121	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7179971	0.91[EUR][1000 genomes]
rs7180093	0.91[EUR][1000 genomes]
rs73405349	0.83[EUR][1000 genomes]
rs73405355	0.83[EUR][1000 genomes]
rs73405356	0.83[EUR][1000 genomes]
rs73405364	0.85[EUR][1000 genomes]
rs73405388	0.83[EUR][1000 genomes]
rs7342575	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs74015721	0.83[EUR][1000 genomes]
rs74015757	0.86[EUR][1000 genomes]
rs74015761	0.86[EUR][1000 genomes]
rs74016407	1.00[AMR][1000 genomes]
rs74016414	1.00[AMR][1000 genomes]
rs8034090	1.00[YRI][hapmap]
rs8036648	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038895	1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51974200-52018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:51974600-52016400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:51975600-52017200	Weak transcription	Fetal Brain Male	brain
4	chr15:51983000-52013200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:51984800-52018600	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:51990000-52016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:51991400-52018800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:51992200-52018800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:51993600-52016800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:51995400-52013200	Weak transcription	Brain Substantia Nigra	brain
11	chr15:51999800-52018200	Weak transcription	Fetal Stomach	stomach
12	chr15:52000000-52013800	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:52000800-52024000	Weak transcription	Gastric	stomach
14	chr15:52001000-52018600	Weak transcription	Pancreas	Pancrea
15	chr15:52001200-52013000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:52001600-52012000	Weak transcription	Primary B cells from cord blood	blood
17	chr15:52002400-52013600	Strong transcription	Fetal Brain Female	brain
18	chr15:52002800-52016600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:52003400-52013200	Weak transcription	Aorta	Aorta
20	chr15:52004000-52013400	Strong transcription	Brain Germinal Matrix	brain
21	chr15:52004400-52016400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:52004800-52012600	Weak transcription	Primary T cells from cord blood	blood
23	chr15:52004800-52018600	Weak transcription	Spleen	Spleen
24	chr15:52006200-52013000	Weak transcription	Esophagus	oesophagus
25	chr15:52006400-52013800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:52006400-52018400	Weak transcription	Fetal Muscle Leg	muscle
27	chr15:52006600-52012000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:52006800-52013400	Weak transcription	K562	blood
29	chr15:52007000-52023400	Weak transcription	Brain Anterior Caudate	brain
30	chr15:52007400-52013000	Weak transcription	Dnd41	blood
31	chr15:52007400-52013400	Enhancers	Fetal Intestine Large	intestine
32	chr15:52007600-52013400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:52007600-52016800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:52007800-52016800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:52007800-52018200	Weak transcription	NHDF-Ad	bronchial
36	chr15:52008000-52013400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:52008200-52023200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:52008400-52018400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:52008400-52023400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:52008800-52012800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:52008800-52016600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:52009000-52012400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr15:52009000-52013400	Weak transcription	Brain Angular Gyrus	brain
44	chr15:52009000-52016600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:52009600-52011800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:52009600-52014000	Enhancers	Fetal Intestine Small	intestine
47	chr15:52010000-52013000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:52010000-52013400	Enhancers	Duodenum Mucosa	Duodenum
49	chr15:52010000-52013600	Weak transcription	Stomach Mucosa	stomach
50	chr15:52010600-52012800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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