Variant report

Variant	rs2530664
Chromosome Location	chr22:30038152-30038153
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30019747..30021747-chr22:30036683..30039570,2	MCF-7	breast:
2	chr22:30036794..30038709-chr22:30046357..30049323,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1006396	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10427824	0.91[AFR][1000 genomes]
rs1049534	0.86[JPT][hapmap]
rs11704899	0.94[CEU][hapmap];0.90[TSI][hapmap]
rs11705569	0.87[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs16987752	1.00[YRI][hapmap]
rs16987832	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2072303	1.00[YRI][hapmap]
rs2074947	1.00[YRI][hapmap]
rs2074948	0.86[JPT][hapmap]
rs2074949	1.00[YRI][hapmap]
rs2074950	1.00[YRI][hapmap]
rs2247753	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];0.99[ASN][1000 genomes]
rs2267146	1.00[YRI][hapmap]
rs2267152	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs2270079	1.00[YRI][hapmap]
rs2302140	1.00[YRI][hapmap]
rs2302141	0.86[JPT][hapmap]
rs2302142	1.00[YRI][hapmap]
rs2527336	0.87[CEU][hapmap]
rs2530656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2530658	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2531848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2531849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456285	0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs456585	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs458196	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs460428	0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs462444	0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs463220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs468254	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs468692	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs468795	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs468852	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs469363	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs5763297	0.86[JPT][hapmap]
rs5763301	0.86[JPT][hapmap];0.82[TSI][hapmap]
rs5763303	0.86[JPT][hapmap]
rs5763305	0.94[CEU][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs5763306	0.86[JPT][hapmap]
rs57995869	0.91[AFR][1000 genomes]
rs7609	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs8135828	0.94[CEU][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2530664	THOC5	cis	Muscle Skeletal	GTEx
rs2530664	THOC5	cis	lung	GTEx
rs2530664	THOC5	cis	Artery Aorta	GTEx
rs2530664	CABP7	cis	cerebellum	SCAN
rs2530664	THOC5	cis	Adipose Subcutaneous	GTEx
rs2530664	NIPSNAP1	cis	cerebellum	SCAN
rs2530664	THOC5	cis	Artery Tibial	GTEx
rs2530664	THOC5	cis	Esophagus Muscularis	GTEx
rs2530664	THOC5	cis	Nerve Tibial	GTEx
rs2530664	NIPSNAP1	cis	Stomach	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30018000-30069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:30020200-30057000	Weak transcription	Psoas Muscle	Psoas
4	chr22:30020200-30064200	Weak transcription	Small Intestine	intestine
5	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
6	chr22:30021800-30041600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr22:30022000-30038400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr22:30022200-30053400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr22:30023200-30038600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr22:30023800-30038200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr22:30023800-30038600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr22:30024200-30038200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr22:30026800-30038200	Weak transcription	Spleen	Spleen
14	chr22:30026800-30055800	Weak transcription	Gastric	stomach
15	chr22:30027200-30044400	Weak transcription	Brain Substantia Nigra	brain
16	chr22:30027600-30038200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr22:30027600-30057200	Weak transcription	Brain Hippocampus Middle	brain
18	chr22:30027800-30056000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr22:30028400-30044400	Weak transcription	Pancreas	Pancrea
20	chr22:30029600-30053800	Weak transcription	Esophagus	oesophagus
21	chr22:30030000-30038400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr22:30032200-30047000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr22:30032200-30057000	Weak transcription	Colonic Mucosa	Colon
24	chr22:30032200-30070000	Weak transcription	Fetal Brain Male	brain
25	chr22:30032400-30039200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr22:30032400-30039400	Strong transcription	Primary T cells from cord blood	blood
27	chr22:30032600-30039200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr22:30032800-30039200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr22:30032800-30039400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr22:30033000-30039000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr22:30033000-30039000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr22:30033000-30039000	Strong transcription	NHEK	skin
33	chr22:30033000-30053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr22:30033200-30038200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr22:30033200-30038200	Weak transcription	Brain Germinal Matrix	brain
36	chr22:30033400-30039000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr22:30033400-30039000	Strong transcription	NH-A	brain
38	chr22:30033400-30039600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr22:30033600-30039000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr22:30033800-30039000	Strong transcription	Fetal Lung	lung
41	chr22:30033800-30039200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr22:30033800-30039200	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr22:30033800-30039200	Strong transcription	Osteobl	bone
44	chr22:30033800-30039600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr22:30034000-30039800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr22:30034200-30040800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr22:30034400-30060400	Weak transcription	K562	blood
48	chr22:30034800-30039000	Genic enhancers	GM12878-XiMat	blood
49	chr22:30035200-30039400	Strong transcription	Fetal Stomach	stomach
50	chr22:30035400-30047400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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