Variant report

Variant	rs1345741
Chromosome Location	chr5:147755119-147755120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:147754412..147757315-chr5:147760463..147763292,2	MCF-7	breast:
2	chr5:147693480..147694147-chr5:147754027..147755262,3	K562	blood:
3	chr5:147752174..147758747-chr5:147760816..147763342,8	K562	blood:
4	chr5:147754191..147756120-chr5:147761410..147763004,2	K562	blood:
5	chr5:147754004..147757324-chr5:147763355..147766181,3	K562	blood:
6	chr5:147753458..147755504-chr5:147763355..147765136,2	K562	blood:

Variant related genes	Relation type
ENSG00000145879	Chromatin interaction
ENSG00000145868	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10035818	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10036053	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10041283	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs10043775	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs10044054	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10044061	0.86[CEU][hapmap]
rs10050560	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10051223	0.93[ASW][hapmap];0.86[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes]
rs10055332	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10055430	0.86[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs10057472	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10068216	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs10068891	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs10072051	0.82[CEU][hapmap]
rs10072958	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs10079420	0.86[AMR][1000 genomes]
rs10476892	0.86[EUR][1000 genomes]
rs10477374	0.86[EUR][1000 genomes]
rs10477376	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs11168046	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes]
rs11168047	0.86[AMR][1000 genomes]
rs1128450	0.84[AMR][1000 genomes]
rs12513547	0.82[CEU][hapmap]
rs12521065	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs12717971	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13153619	0.86[EUR][1000 genomes]
rs13176114	0.83[EUR][1000 genomes]
rs1363704	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1363705	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1363707	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1422968	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1422970	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1422976	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1422977	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1582519	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs17108251	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs17719578	0.83[EUR][1000 genomes]
rs17719662	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17719763	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17719873	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17720155	0.86[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17776674	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17776882	0.86[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1862430	0.83[EUR][1000 genomes]
rs1862431	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1984789	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes]
rs2112761	0.93[ASW][hapmap];0.86[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2161432	0.86[EUR][1000 genomes]
rs2216653	0.86[EUR][1000 genomes]
rs2400509	0.86[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2400510	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs28442279	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2895761	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34001290	0.85[EUR][1000 genomes]
rs34163281	0.83[EUR][1000 genomes]
rs35700061	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35792476	0.83[EUR][1000 genomes]
rs3734120	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs3734121	0.81[AMR][1000 genomes]
rs3749689	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3749690	0.86[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs3925019	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4349707	0.81[CEU][hapmap]
rs4406123	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4599524	0.86[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4599526	0.95[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4639213	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4705247	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705248	0.82[CEU][hapmap];0.84[TSI][hapmap]
rs4705249	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705252	0.86[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs4705253	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580542	0.83[EUR][1000 genomes]
rs6580544	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580545	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580546	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580548	0.86[EUR][1000 genomes]
rs6860261	0.85[EUR][1000 genomes]
rs6861078	0.93[ASW][hapmap];0.86[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes]
rs6865036	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6865972	0.85[EUR][1000 genomes]
rs6866106	0.86[EUR][1000 genomes]
rs6875252	0.83[EUR][1000 genomes]
rs6875795	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6876308	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6876982	0.82[CEU][hapmap]
rs6882932	0.82[EUR][1000 genomes]
rs6886203	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6891724	0.86[EUR][1000 genomes]
rs6892647	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6893378	0.85[EUR][1000 genomes]
rs6894032	0.86[EUR][1000 genomes]
rs7712350	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7713927	0.82[AMR][1000 genomes]
rs7713986	0.83[EUR][1000 genomes]
rs7716578	0.86[EUR][1000 genomes]
rs7727320	0.82[AMR][1000 genomes]
rs7728004	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7729309	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs7730707	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7734458	0.86[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7736019	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7736728	0.86[EUR][1000 genomes]
rs9325095	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs9325096	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9325098	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs9784645	0.83[EUR][1000 genomes]
rs999741	0.86[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1345741	SPINK9	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147729200-147762200	Weak transcription	Aorta	Aorta
2	chr5:147747800-147762400	Weak transcription	Ovary	ovary
3	chr5:147748200-147756800	Weak transcription	Fetal Brain Female	brain
4	chr5:147749600-147757400	Weak transcription	Psoas Muscle	Psoas
5	chr5:147749800-147757400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:147749800-147762200	Weak transcription	Adipose Nuclei	Adipose
7	chr5:147750000-147756600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:147750000-147762400	Weak transcription	Brain Substantia Nigra	brain
9	chr5:147750400-147756600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:147751200-147761800	Weak transcription	Fetal Brain Male	brain
11	chr5:147751400-147756800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:147751400-147763000	Weak transcription	Esophagus	oesophagus
13	chr5:147751800-147762400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:147752200-147756600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:147752200-147756800	Weak transcription	Gastric	stomach
16	chr5:147752200-147760800	Weak transcription	Fetal Lung	lung
17	chr5:147752600-147761000	Weak transcription	Brain Germinal Matrix	brain
18	chr5:147752600-147762200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:147752600-147762600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:147752800-147762600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:147752800-147762800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:147753200-147755200	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:147753200-147755400	Weak transcription	Right Ventricle	heart
24	chr5:147753200-147756600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:147753200-147757000	Weak transcription	Primary B cells from cord blood	blood
26	chr5:147753200-147762200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:147753600-147756600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:147753600-147756600	Weak transcription	Liver	Liver
29	chr5:147754200-147755400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:147754200-147756200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr5:147754400-147762200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:147754400-147762200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:147754400-147762400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:147754600-147757400	Weak transcription	Left Ventricle	heart
35	chr5:147754600-147762400	Weak transcription	Stomach Mucosa	stomach
36	chr5:147754800-147756600	Weak transcription	Brain Anterior Caudate	brain
37	chr5:147754800-147758200	Weak transcription	Fetal Intestine Small	intestine
38	chr5:147754800-147762400	Weak transcription	Fetal Intestine Large	intestine
39	chr5:147755000-147755800	Flanking Active TSS	Fetal Heart	heart
40	chr5:147755000-147756600	Weak transcription	Brain Hippocampus Middle	brain
41	chr5:147755000-147758000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:147755000-147762000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:147755000-147762200	Weak transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links