Variant report

Variant	rs12693016
Chromosome Location	chr2:173860313-173860314
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173859166..173862037-chr2:173939692..173943605,3	MCF-7	breast:
2	chr2:173849142..173852598-chr2:173855356..173861233,5	MCF-7	breast:
3	chr2:173859019..173861377-chr2:173862387..173864335,2	MCF-7	breast:
4	chr2:173853861..173856842-chr2:173857808..173860672,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1011345	0.98[ASN][1000 genomes]
rs11687902	0.98[ASN][1000 genomes]
rs11687990	0.98[ASN][1000 genomes]
rs11885983	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12616563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12624093	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12693015	0.91[ASN][1000 genomes]
rs12996130	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13000260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13413796	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446981	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs16861125	0.98[ASN][1000 genomes]
rs16861148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16861173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17302307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17374295	1.00[ASN][1000 genomes]
rs1823151	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1979186	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2121483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2166588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2242079	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2258918	0.83[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305461	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2592944	0.83[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2602217	0.83[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2676521	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3754753	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3769225	0.95[ASN][1000 genomes]
rs3769226	0.95[ASN][1000 genomes]
rs3769227	0.92[ASN][1000 genomes]
rs3769228	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3769229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3769231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3769236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3820840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3820841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3820843	0.98[ASN][1000 genomes]
rs3820844	0.98[ASN][1000 genomes]
rs4972523	0.98[ASN][1000 genomes]
rs66487735	0.98[ASN][1000 genomes]
rs718902	0.88[ASN][1000 genomes]
rs72896070	0.97[ASN][1000 genomes]
rs72909440	0.95[ASN][1000 genomes]
rs72909444	0.95[ASN][1000 genomes]
rs72909446	0.95[ASN][1000 genomes]
rs7585997	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7603772	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

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	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12693016	LRP2	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173833800-173860800	Weak transcription	Right Ventricle	heart
2	chr2:173835800-173886800	Weak transcription	Lung	lung
3	chr2:173843200-173861400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:173849800-173861200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:173850400-173864600	Weak transcription	Psoas Muscle	Psoas
6	chr2:173851000-173860400	Weak transcription	Fetal Heart	heart
7	chr2:173851000-173861000	Weak transcription	Fetal Kidney	kidney
8	chr2:173852400-173868000	Weak transcription	Gastric	stomach
9	chr2:173855800-173860400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:173855800-173860400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:173855800-173863400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:173856000-173885200	Weak transcription	Brain Anterior Caudate	brain
13	chr2:173856200-173861400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:173856200-173861400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:173856200-173862000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:173856200-173863600	Weak transcription	Brain Germinal Matrix	brain
17	chr2:173856200-173882400	Weak transcription	Left Ventricle	heart
18	chr2:173856200-173892600	Weak transcription	Brain Angular Gyrus	brain
19	chr2:173856400-173860400	Weak transcription	Fetal Lung	lung
20	chr2:173856400-173860600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:173857400-173861400	Weak transcription	Liver	Liver
22	chr2:173857800-173860400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:173858000-173862000	Enhancers	HepG2	liver
24	chr2:173858200-173860600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:173858200-173862000	Enhancers	Ovary	ovary
26	chr2:173858400-173862000	Enhancers	HSMMtube	muscle
27	chr2:173858400-173869000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:173858600-173861800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:173858600-173862600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:173858800-173860800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:173859200-173860600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:173859200-173860800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr2:173859200-173863200	Weak transcription	Placenta	Placenta
34	chr2:173859400-173860600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:173859400-173860600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr2:173859600-173861000	Enhancers	Fetal Stomach	stomach
37	chr2:173859600-173861000	Enhancers	Stomach Mucosa	stomach
38	chr2:173859600-173862000	Enhancers	NHDF-Ad	bronchial
39	chr2:173859600-173862200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:173859800-173860400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:173859800-173860800	Enhancers	Adipose Nuclei	Adipose
42	chr2:173859800-173862600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:173860000-173860400	Enhancers	Fetal Muscle Trunk	muscle
44	chr2:173860200-173860400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:173860200-173860600	Flanking Active TSS	A549	lung
46	chr2:173860200-173861200	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:173860200-173861800	Enhancers	Hela-S3	cervix
48	chr2:173860200-173862000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:173860200-173862000	Enhancers	HSMM	muscle
50	chr2:173860200-173862200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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