Variant report

Variant	rs7989175
Chromosome Location	chr13:49663915-49663916
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49657055..49658682-chr13:49662572..49665462,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs12872974	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1359066	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1407827	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1407829	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1535922	0.82[CHB][hapmap]
rs1928109	0.91[CHB][hapmap]
rs1937180	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap]
rs1937181	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs1983805	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs2021622	0.99[ASN][1000 genomes]
rs2026029	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[YRI][hapmap]
rs2146748	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2149498	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap]
rs2181537	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2181538	1.00[ASN][1000 genomes]
rs2181539	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2183095	0.91[CHB][hapmap]
rs2224742	0.90[ASN][1000 genomes]
rs2407266	0.91[CHB][hapmap]
rs2897633	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2897689	0.92[ASW][hapmap];0.93[CHD][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs2987528	0.91[CHB][hapmap]
rs2987532	0.91[CHB][hapmap]
rs2994377	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs2994378	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs2994379	0.91[CHB][hapmap]
rs2994380	0.91[CHB][hapmap]
rs3012116	0.91[CHB][hapmap]
rs3012117	0.91[CHB][hapmap]
rs3012121	0.91[CHB][hapmap]
rs3012127	0.91[CHB][hapmap]
rs3012133	0.91[CHB][hapmap]
rs3012136	0.91[CHB][hapmap]
rs4142065	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4258502	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs4530025	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4942796	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs4942799	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs4942800	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs6561493	1.00[ASN][1000 genomes]
rs6561496	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6561497	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6561504	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs720627	0.91[CHB][hapmap]
rs728075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs7318871	1.00[ASN][1000 genomes]
rs7328000	0.83[ASN][1000 genomes]
rs7329291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs7331917	0.86[ASN][1000 genomes]
rs7333097	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7333285	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs7338529	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7983885	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs7986624	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7987258	0.85[ASW][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.95[YRI][hapmap]
rs7988168	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7994368	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs7994910	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7995616	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs7997118	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7998359	0.90[CHB][hapmap]
rs7999513	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8248	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs9316426	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9316428	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9316429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9526518	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs9526520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9535126	0.91[CHB][hapmap]
rs9535136	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9535140	0.97[ASN][1000 genomes]
rs9535141	0.96[ASN][1000 genomes]
rs9535145	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs9535146	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9535147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs9535149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9535154	0.91[CHB][hapmap]
rs9535155	0.91[CHB][hapmap]
rs9535156	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9535166	0.91[CHB][hapmap]
rs9535167	0.91[CHB][hapmap]
rs9562866	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9562870	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.90[YRI][hapmap]
rs9568143	0.83[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs9568150	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9568151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9568154	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9591235	0.82[ASN][1000 genomes]
rs972297	0.80[CHD][hapmap]

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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv976274	chr13:49655803-49666815	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1035	chr13:49656225-49700371	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7989175	CAB39L	cis	cerebellum	SCAN
rs7989175	RCBTB1	cis	cerebellum	SCAN
rs7989175	RCBTB1	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49627400-49672400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:49629000-49665600	Weak transcription	Lung	lung
3	chr13:49629600-49665400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr13:49630400-49664000	Weak transcription	Fetal Intestine Small	intestine
5	chr13:49632200-49664800	Weak transcription	Fetal Lung	lung
6	chr13:49635000-49664400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr13:49636800-49667800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr13:49639600-49687200	Weak transcription	Pancreas	Pancrea
9	chr13:49640600-49683800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr13:49641800-49671600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr13:49645000-49671000	Weak transcription	Small Intestine	intestine
12	chr13:49649400-49684200	Weak transcription	Right Ventricle	heart
13	chr13:49649800-49671600	Weak transcription	Brain Hippocampus Middle	brain
14	chr13:49651400-49665600	Weak transcription	Fetal Thymus	thymus
15	chr13:49651400-49666800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr13:49651600-49670200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:49651600-49670800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr13:49651800-49664800	Weak transcription	Fetal Stomach	stomach
19	chr13:49651800-49665000	Weak transcription	Fetal Muscle Leg	muscle
20	chr13:49651800-49671000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr13:49651800-49671800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr13:49651800-49684000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr13:49651800-49684000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr13:49652000-49667600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr13:49652000-49671000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr13:49652400-49671600	Weak transcription	Spleen	Spleen
27	chr13:49655200-49667400	Weak transcription	HepG2	liver
28	chr13:49655600-49684200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr13:49656000-49673000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr13:49657200-49671600	Weak transcription	Ovary	ovary
31	chr13:49657200-49672200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr13:49657200-49692400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr13:49657400-49665600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr13:49657400-49668200	Weak transcription	Thymus	Thymus
35	chr13:49657400-49670800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr13:49657400-49670800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr13:49657400-49670800	Weak transcription	Aorta	Aorta
38	chr13:49657400-49671200	Weak transcription	HSMM	muscle
39	chr13:49657400-49671600	Weak transcription	Left Ventricle	heart
40	chr13:49657400-49674800	Weak transcription	Fetal Intestine Large	intestine
41	chr13:49657400-49674800	Weak transcription	Placenta	Placenta
42	chr13:49657400-49684000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr13:49657600-49670200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr13:49657600-49670800	Weak transcription	Liver	Liver
45	chr13:49657800-49683800	Weak transcription	Primary B cells from cord blood	blood
46	chr13:49658000-49665600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr13:49658000-49671000	Weak transcription	HSMMtube	muscle
48	chr13:49658000-49671400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr13:49658800-49671600	Weak transcription	Colon Smooth Muscle	Colon
50	chr13:49659400-49666600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links