Variant report

Variant	rs7302981
Chromosome Location	chr12:50537815-50537816
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50529645..50533801-chr12:50534954..50538460,5	MCF-7	breast:
2	chr12:50467353..50469226-chr12:50536812..50539286,2	MCF-7	breast:
3	chr12:50525700..50528015-chr12:50536583..50539181,2	MCF-7	breast:
4	chr12:50478449..50481902-chr12:50536030..50539935,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066117	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1044370	0.90[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10747570	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169294	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169300	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11831413	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12426261	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12815871	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12824125	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12830386	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1862043	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2178173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2358538	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.90[YRI][hapmap]
rs34573394	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35549836	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35998534	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4459386	0.89[ASW][hapmap];0.89[YRI][hapmap]
rs4883481	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4883482	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56709084	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs646782	1.00[CHB][hapmap]
rs6580729	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66768395	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs706791	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs706792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs706793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7136570	1.00[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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7279	1.00[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];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7294548	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297421	1.00[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];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7301649	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7301740	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7308356	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7532	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7957659	0.89[ASW][hapmap];0.85[LWK][hapmap];0.89[YRI][hapmap]
rs7967705	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7967844	0.93[EUR][1000 genomes]
rs7972842	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836172	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs836177	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs836179	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs836180	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs844347	0.84[GIH][hapmap]
rs860698	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]

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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7302981	LASS5	cis	cerebellum	SCAN
rs7302981	LASS5	cis	multi-tissue	Pritchard
rs7302981	MCRS1	cis	parietal	SCAN
rs7302981	SNORA2A	cis	parietal	SCAN
rs7302981	LASS5	cis	parietal	SCAN
rs7302981	CERS5	cis	Nerve Tibial	GTEx
rs7302981	DIP2B	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
2	chr12:50511200-50538200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:50511400-50538600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:50512600-50538200	Strong transcription	Primary B cells from cord blood	blood
5	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:50519200-50538200	Strong transcription	Fetal Muscle Leg	muscle
7	chr12:50519400-50538400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:50519600-50538200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr12:50520200-50539000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:50520400-50538000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:50520600-50538000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:50520600-50538200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:50520600-50538200	Strong transcription	Fetal Thymus	thymus
14	chr12:50520600-50538400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:50520600-50538600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:50520600-50538600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:50520800-50538200	Strong transcription	Thymus	Thymus
18	chr12:50521200-50538400	Strong transcription	HSMMtube	muscle
19	chr12:50521600-50538400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:50522800-50538200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:50522800-50538400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:50522800-50538600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:50523400-50538600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:50523800-50538400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr12:50524000-50538600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr12:50524000-50559800	Weak transcription	Right Atrium	heart
27	chr12:50524600-50541600	Weak transcription	Psoas Muscle	Psoas
28	chr12:50527400-50538200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:50528800-50538000	Weak transcription	Hela-S3	cervix
30	chr12:50528800-50543000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:50529200-50538200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:50529200-50538400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:50529400-50538000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:50529600-50538200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:50529600-50542800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:50529800-50543000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:50529800-50559800	Weak transcription	NHLF	lung
38	chr12:50530000-50538200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:50530000-50538800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:50530000-50539600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:50530000-50559600	Weak transcription	A549	lung
42	chr12:50530000-50560200	Weak transcription	Esophagus	oesophagus
43	chr12:50531200-50548400	Weak transcription	HUVEC	blood vessel
44	chr12:50531600-50538200	Strong transcription	Fetal Stomach	stomach
45	chr12:50531600-50543200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:50531600-50558200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr12:50531800-50544600	Weak transcription	Fetal Kidney	kidney
48	chr12:50531800-50554400	Weak transcription	K562	blood
49	chr12:50531800-50558400	Weak transcription	Fetal Brain Male	brain
50	chr12:50532000-50539600	Weak transcription	Brain Substantia Nigra	brain

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