Variant report

Variant	rs9567986
Chromosome Location	chr13:48618170-48618171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:48612381..48615273-chr13:48617254..48619078,2	MCF-7	breast:
2	chr13:48611908..48615197-chr13:48616431..48620748,8	K562	blood:
3	chr13:48615412..48618304-chr13:48618924..48621110,2	K562	blood:

Variant related genes	Relation type
ENSG00000136143	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1041070	0.81[ASN][1000 genomes]
rs1098354	0.85[ASN][1000 genomes]
rs11148100	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11618397	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1185727	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12428259	0.85[CHB][hapmap]
rs12429137	0.86[CHB][hapmap]
rs12431098	0.86[CHD][hapmap]
rs1326135	0.83[ASN][1000 genomes]
rs1326136	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs1326140	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1536301	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs1544078	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17071168	0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1886975	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2031590	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2094194	0.80[ASN][1000 genomes]
rs2148243	0.82[ASN][1000 genomes]
rs2148244	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2182376	0.84[ASN][1000 genomes]
rs2296574	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs2406693	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2406697	0.84[ASN][1000 genomes]
rs2406698	0.80[ASN][1000 genomes]
rs4245347	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4447314	0.84[ASN][1000 genomes]
rs4522322	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4941619	0.85[CHB][hapmap]
rs4941621	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4942726	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4942727	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4942728	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4942729	0.82[ASN][1000 genomes]
rs4942730	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4942735	0.83[ASN][1000 genomes]
rs4942739	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61973260	0.83[EUR][1000 genomes]
rs6561419	0.82[ASN][1000 genomes]
rs6561420	0.82[ASN][1000 genomes]
rs6561424	0.83[ASN][1000 genomes]
rs6561427	0.83[ASN][1000 genomes]
rs6561429	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs6561430	0.83[ASN][1000 genomes]
rs6561431	0.86[ASN][1000 genomes]
rs6561432	0.86[ASN][1000 genomes]
rs7318770	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7319245	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7320366	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs7322515	0.82[ASN][1000 genomes]
rs7325189	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7325437	0.86[ASN][1000 genomes]
rs7326889	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7326984	0.82[ASN][1000 genomes]
rs7327730	0.84[ASN][1000 genomes]
rs7328525	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7328537	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7329419	0.81[ASN][1000 genomes]
rs7330130	0.86[ASN][1000 genomes]
rs7330913	0.83[ASN][1000 genomes]
rs7331285	0.86[ASN][1000 genomes]
rs7332304	0.86[ASN][1000 genomes]
rs7333659	0.81[ASN][1000 genomes]
rs7336972	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7337004	0.86[ASN][1000 genomes]
rs7337744	0.83[ASN][1000 genomes]
rs7338125	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7338373	0.86[ASN][1000 genomes]
rs765809	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7989231	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7990244	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7990266	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7990505	0.82[ASN][1000 genomes]
rs7994359	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7996580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7997802	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7998116	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7998260	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7998497	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7998998	0.84[ASN][1000 genomes]
rs7999360	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs8000164	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8001432	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316339	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9316343	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316344	0.84[ASN][1000 genomes]
rs9526422	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526429	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9526430	0.84[ASN][1000 genomes]
rs9526433	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526434	0.83[ASN][1000 genomes]
rs9534876	0.95[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9534877	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9534878	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9534881	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9534889	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs9534892	0.80[ASN][1000 genomes]
rs9534898	0.83[ASN][1000 genomes]
rs9534901	0.83[ASN][1000 genomes]
rs9534903	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9534904	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9534905	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9534906	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9534907	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9534908	0.84[ASN][1000 genomes]
rs9534909	0.83[ASN][1000 genomes]
rs9534912	0.84[ASN][1000 genomes]
rs9534913	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9534918	0.86[EUR][1000 genomes]
rs9534919	0.86[EUR][1000 genomes]
rs9534922	0.81[ASN][1000 genomes]
rs9534923	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9534926	0.84[ASN][1000 genomes]
rs9534929	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9567954	0.81[ASN][1000 genomes]
rs9567955	0.81[ASN][1000 genomes]
rs9567958	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9567960	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9567964	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9567972	0.83[ASN][1000 genomes]
rs9567976	0.84[ASN][1000 genomes]
rs9567980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9595815	0.93[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs9595825	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9567986	ENOX1	cis	cerebellum	SCAN
rs9567986	MED4	cis	parietal	SCAN
rs9567986	SUCLA2	cis	cerebellum	SCAN
rs9567986	SUCLA2	cis	parietal	SCAN
rs9567986	DLEU1	cis	parietal	SCAN
rs9567986	MED4	cis	multi-tissue	Pritchard
rs9567986	ZC3H13	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48612400-48625000	Weak transcription	Spleen	Spleen
2	chr13:48612600-48623000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:48612600-48624200	Weak transcription	Gastric	stomach
4	chr13:48612600-48624800	Weak transcription	Ovary	ovary
5	chr13:48612600-48631600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:48612600-48640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr13:48612600-48645000	Weak transcription	Stomach Mucosa	stomach
8	chr13:48612800-48620800	Weak transcription	Primary B cells from cord blood	blood
9	chr13:48612800-48622000	Weak transcription	Brain Germinal Matrix	brain
10	chr13:48612800-48622000	Weak transcription	Placenta	Placenta
11	chr13:48612800-48622200	Weak transcription	Fetal Brain Female	brain
12	chr13:48612800-48622400	Weak transcription	Brain Substantia Nigra	brain
13	chr13:48612800-48624600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr13:48612800-48624800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr13:48612800-48625000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr13:48612800-48628000	Weak transcription	Fetal Brain Male	brain
17	chr13:48612800-48640200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr13:48612800-48640400	Weak transcription	Psoas Muscle	Psoas
19	chr13:48613000-48621800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr13:48613000-48622200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr13:48613000-48640200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr13:48613000-48640400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr13:48613200-48624800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr13:48613200-48624800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr13:48613200-48626600	Weak transcription	Right Ventricle	heart
26	chr13:48613200-48629000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:48613200-48631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr13:48613200-48640400	Weak transcription	Fetal Heart	heart
29	chr13:48613200-48641600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr13:48613200-48642200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:48613400-48618200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr13:48613400-48624800	Weak transcription	Brain Anterior Caudate	brain
33	chr13:48613400-48625800	Weak transcription	K562	blood
34	chr13:48613400-48641600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr13:48613400-48647000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr13:48613600-48622200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:48613600-48625200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr13:48613600-48636400	Weak transcription	Hela-S3	cervix
39	chr13:48613600-48645000	Weak transcription	Small Intestine	intestine
40	chr13:48614400-48618200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr13:48614400-48627600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr13:48614400-48628600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr13:48614400-48636400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr13:48614600-48618800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr13:48614800-48628200	Strong transcription	Dnd41	blood
46	chr13:48615000-48623200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr13:48615000-48623800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr13:48615200-48618400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr13:48615200-48618800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr13:48615200-48618800	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links