Variant report

Variant	rs7998427
Chromosome Location	chr13:50050620-50050621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12050042	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs1409016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543514	0.83[EUR][1000 genomes]
rs1555530	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1980794	0.97[ASN][1000 genomes]
rs1980795	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.97[ASN][1000 genomes]
rs1998782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2057413	0.81[EUR][1000 genomes]
rs2057415	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2057417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407689	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2407692	0.86[EUR][1000 genomes]
rs3764085	0.97[ASN][1000 genomes]
rs3764090	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs3764091	0.81[EUR][1000 genomes]
rs3794381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4142285	0.81[EUR][1000 genomes]
rs4468500	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4941642	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4942831	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942832	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6561525	0.86[EUR][1000 genomes]
rs71188363	0.90[ASN][1000 genomes]
rs7139634	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs721458	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7318481	0.88[YRI][hapmap]
rs7321228	0.81[EUR][1000 genomes]
rs7321670	0.83[EUR][1000 genomes]
rs7328782	0.84[EUR][1000 genomes]
rs7329078	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7330512	0.81[EUR][1000 genomes]
rs7338755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7982297	0.83[EUR][1000 genomes]
rs7982598	0.83[EUR][1000 genomes]
rs7987293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7992603	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs7994115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994130	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7994566	0.90[CEU][hapmap]
rs7996852	0.82[EUR][1000 genomes]
rs7998022	0.81[EUR][1000 genomes]
rs7998660	0.81[EUR][1000 genomes]
rs9316453	0.81[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs9526564	0.81[EUR][1000 genomes]
rs9526569	0.90[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap]
rs9535248	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568219	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568223	0.97[ASN][1000 genomes]
rs959421	0.81[EUR][1000 genomes]
rs967163	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs967164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv430558	chr13:49914393-50059354	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430559	chr13:49930369-50059354	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430560	chr13:49930643-50059354	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv430562	chr13:49930643-50067246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv430564	chr13:49945247-50059354	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv430571	chr13:49961137-50059354	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv523648	chr13:50005444-50086266	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv561613	chr13:50013622-50086266	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv900070	chr13:50013622-50087142	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv561614	chr13:50042983-50086253	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv561615	chr13:50042983-50086266	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7998427	RB1	cis	cerebellum	SCAN
rs7998427	ST13P4	cis	cerebellum	SCAN
rs7998427	SETDB2	cis	cerebellum	SCAN
rs7998427	PHF11	Cis_1M	lymphoblastoid	RTeQTL
rs7998427	LPAR6	cis	parietal	SCAN
rs7998427	SETDB2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50020200-50068400	Weak transcription	HMEC	breast
2	chr13:50022000-50069000	Weak transcription	Fetal Brain Male	brain
3	chr13:50023000-50068000	Weak transcription	Hela-S3	cervix
4	chr13:50031800-50068800	Weak transcription	Psoas Muscle	Psoas
5	chr13:50034400-50050800	Weak transcription	NHEK	skin
6	chr13:50034400-50052200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:50034400-50068800	Weak transcription	NH-A	brain
8	chr13:50036400-50068600	Weak transcription	Stomach Mucosa	stomach
9	chr13:50036600-50068000	Weak transcription	K562	blood
10	chr13:50037800-50050800	Weak transcription	Brain Angular Gyrus	brain
11	chr13:50037800-50051000	Weak transcription	Spleen	Spleen
12	chr13:50037800-50064000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:50037800-50068400	Weak transcription	HUVEC	blood vessel
14	chr13:50037800-50069000	Weak transcription	Colonic Mucosa	Colon
15	chr13:50038000-50050800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr13:50038000-50051200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr13:50038000-50062800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr13:50038000-50063400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr13:50038000-50063600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr13:50038000-50063800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr13:50038000-50068800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr13:50038200-50050800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr13:50038200-50051000	Weak transcription	Aorta	Aorta
24	chr13:50038200-50054200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr13:50038200-50062400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr13:50038200-50063400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr13:50038400-50050800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr13:50038400-50062200	Strong transcription	Primary T cells from cord blood	blood
29	chr13:50038400-50066800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr13:50038400-50066800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr13:50038400-50069000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr13:50038400-50069400	Weak transcription	Small Intestine	intestine
33	chr13:50038600-50051000	Weak transcription	Brain Germinal Matrix	brain
34	chr13:50038600-50052200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr13:50038600-50053000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr13:50038600-50068800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr13:50038800-50069000	Weak transcription	HSMM	muscle
38	chr13:50039000-50068200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr13:50039200-50068800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr13:50039400-50053200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr13:50039400-50069200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr13:50040600-50064800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr13:50041000-50068800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr13:50041400-50056000	Strong transcription	Primary B cells from cord blood	blood
45	chr13:50041400-50069400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr13:50041600-50051200	Weak transcription	Pancreas	Pancrea
47	chr13:50041600-50063800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr13:50042000-50063400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr13:50042200-50067000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr13:50042800-50056400	Strong transcription	Fetal Thymus	thymus

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