Variant report

Variant	rs2288487
Chromosome Location	chr16:71509588-71509589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71508819..71510748-chr16:71511995..71514492,2	K562	blood:
2	chr16:71508758..71510611-chr16:71516213..71518587,2	MCF-7	breast:
3	chr16:71507450..71511299-chr16:71511883..71513820,5	K562	blood:
4	chr16:71501449..71503485-chr16:71506644..71509669,3	MCF-7	breast:
5	chr16:71494025..71497980-chr16:71506815..71510228,4	K562	blood:
6	chr16:71508246..71511064-chr16:71516547..71519494,2	K562	blood:

Variant related genes	Relation type
ENSG00000167377	Chromatin interaction
ENSG00000247324	Chromatin interaction
ENSG00000157429	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10500558	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11640165	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11641492	0.91[ASN][1000 genomes]
rs11643101	0.82[JPT][hapmap]
rs11643216	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11644434	0.90[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11645711	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11647749	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12446461	0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs13331346	0.94[ASN][1000 genomes]
rs1609868	0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1609869	0.95[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16973266	0.82[CHB][hapmap];0.86[AMR][1000 genomes]
rs2004672	0.89[ASN][1000 genomes]
rs2070832	0.88[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2288486	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2288488	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303788	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2432524	0.88[CHB][hapmap]
rs28372238	0.89[ASN][1000 genomes]
rs310334	0.89[CHB][hapmap];0.92[CHD][hapmap];0.87[ASN][1000 genomes]
rs35373081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35916432	0.84[ASN][1000 genomes]
rs36063092	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3813743	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4149498	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4503795	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4620964	0.84[ASN][1000 genomes]
rs58134724	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58452291	0.82[EUR][1000 genomes]
rs58719913	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6499523	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7184543	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7186241	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7187165	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7187354	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7188342	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7192986	0.82[ASN][1000 genomes]
rs7199026	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7199373	0.94[ASN][1000 genomes]
rs7200335	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7200431	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7202340	0.84[JPT][hapmap]
rs7202662	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7202953	0.91[ASN][1000 genomes]
rs730470	0.95[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs732318	0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs74026831	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74027246	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8044068	0.89[ASN][1000 genomes]
rs8044561	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs8051212	0.94[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs8053662	0.90[ASN][1000 genomes]
rs8058294	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs8058776	0.85[ASN][1000 genomes]
rs8061078	0.94[CHB][hapmap]
rs9302623	0.92[ASN][1000 genomes]
rs9926110	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[ASN][1000 genomes]
rs9928243	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9933680	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs9935426	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9936249	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9940771	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv3411957	chr16:71509290-71510579	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71496600-71511400	Weak transcription	Pancreas	Pancrea
2	chr16:71496800-71512000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr16:71496800-71512200	Weak transcription	Fetal Intestine Small	intestine
4	chr16:71497000-71511800	Weak transcription	Brain Substantia Nigra	brain
5	chr16:71497000-71517400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr16:71497000-71517400	Weak transcription	Fetal Heart	heart
7	chr16:71497000-71517600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr16:71497400-71509600	Weak transcription	Gastric	stomach
9	chr16:71497400-71509800	Weak transcription	Spleen	Spleen
10	chr16:71502800-71517400	Weak transcription	Dnd41	blood
11	chr16:71504400-71509800	Weak transcription	Fetal Kidney	kidney
12	chr16:71504400-71512800	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr16:71504600-71513600	Strong transcription	Stomach Smooth Muscle	stomach
14	chr16:71504800-71512800	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr16:71504800-71513000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr16:71505000-71513000	Strong transcription	Adipose Nuclei	Adipose
17	chr16:71505600-71509800	Weak transcription	GM12878-XiMat	blood
18	chr16:71505800-71509800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr16:71506400-71517400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr16:71507200-71509600	Weak transcription	Brain Hippocampus Middle	brain
21	chr16:71507200-71510000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr16:71507200-71514800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr16:71507200-71517800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr16:71507400-71517800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr16:71507600-71509600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr16:71507600-71512800	Strong transcription	Ovary	ovary
27	chr16:71507600-71513000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr16:71507600-71517400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr16:71507600-71517400	Weak transcription	Fetal Brain Male	brain
30	chr16:71507800-71509600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr16:71507800-71509600	Enhancers	HSMMtube	muscle
32	chr16:71507800-71509600	Enhancers	Osteobl	bone
33	chr16:71507800-71512600	Strong transcription	Fetal Brain Female	brain
34	chr16:71507800-71512800	Strong transcription	Left Ventricle	heart
35	chr16:71507800-71513000	Strong transcription	Aorta	Aorta
36	chr16:71507800-71513000	Strong transcription	Brain Germinal Matrix	brain
37	chr16:71507800-71513000	Strong transcription	Fetal Muscle Leg	muscle
38	chr16:71507800-71513200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr16:71508000-71509600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr16:71508000-71509600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr16:71508000-71509600	Enhancers	NHDF-Ad	bronchial
42	chr16:71508000-71513000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr16:71508200-71509600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr16:71508200-71509600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr16:71508200-71510200	Strong transcription	Primary hematopoietic stem cells	blood
46	chr16:71508200-71513000	Strong transcription	Liver	Liver
47	chr16:71508400-71509600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr16:71508400-71511600	Weak transcription	Fetal Stomach	stomach
49	chr16:71508400-71511800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr16:71508400-71512200	Strong transcription	Placenta	Placenta

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