Variant report

Variant	rs7145309
Chromosome Location	chr14:78342399-78342400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78336910..78339002-chr14:78342253..78344506,3	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10130790	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs10141465	0.82[ASN][1000 genomes]
rs10146144	0.86[ASN][1000 genomes]
rs1107991	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11159290	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11159291	0.87[CHB][hapmap]
rs11159294	0.83[CHB][hapmap]
rs11159298	0.87[CHB][hapmap]
rs11159300	0.87[CHB][hapmap]
rs11159301	0.87[CHB][hapmap]
rs11159302	0.86[CHB][hapmap]
rs11159306	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11159307	0.92[ASW][hapmap];0.91[CEU][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11622297	0.82[CHB][hapmap]
rs11628049	1.00[CHB][hapmap]
rs12587361	0.87[CHB][hapmap]
rs12878904	0.87[CHB][hapmap]
rs12879726	0.83[CHB][hapmap]
rs12884153	0.83[CHB][hapmap]
rs12893815	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2003600	0.87[CHB][hapmap]
rs2010591	0.82[CHB][hapmap]
rs2017927	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2052444	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2080814	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2080815	0.87[CHB][hapmap]
rs2080816	0.87[CHB][hapmap]
rs2080817	0.87[CHB][hapmap]
rs2098583	0.97[ASN][1000 genomes]
rs2098584	0.90[CHB][hapmap]
rs2287648	1.00[ASW][hapmap];0.82[CEU][hapmap];0.87[CHB][hapmap];0.92[LWK][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2364739	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2364741	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2364743	0.87[CHB][hapmap]
rs2364745	0.85[ASN][1000 genomes]
rs2364842	0.83[CHB][hapmap]
rs2886167	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2886168	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs3783962	0.87[CHB][hapmap]
rs3783966	0.87[CHB][hapmap]
rs3783968	0.87[CHB][hapmap]
rs3783969	0.82[CHB][hapmap]
rs3783971	0.85[ASN][1000 genomes]
rs3783974	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs3825691	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs3825692	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4359362	0.83[CHB][hapmap]
rs4371094	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4393507	0.83[CHB][hapmap]
rs4448861	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4899677	0.83[CHB][hapmap]
rs4899678	0.87[CHB][hapmap]
rs4899679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4903654	0.83[CHB][hapmap]
rs4903655	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4903656	0.87[CHB][hapmap]
rs4903658	0.87[CHB][hapmap]
rs4903660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4903661	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4903662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4903663	0.87[CHB][hapmap]
rs4903664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6574406	0.85[ASN][1000 genomes]
rs6574408	0.86[ASN][1000 genomes]
rs6574409	0.88[ASN][1000 genomes]
rs7146020	0.82[CHB][hapmap]
rs7149884	0.87[CHB][hapmap]
rs7149911	0.92[ASW][hapmap];0.91[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7151404	0.90[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs719049	0.83[CHB][hapmap]
rs724263	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs726538	0.83[CHB][hapmap]
rs741573	0.87[CHB][hapmap]
rs741574	0.87[CHB][hapmap]
rs741575	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7493386	0.85[CHB][hapmap]
rs8004053	1.00[ASN][1000 genomes]
rs8006218	0.84[ASN][1000 genomes]
rs8009433	0.87[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap]
rs8009937	0.81[ASN][1000 genomes]
rs8010212	0.90[ASN][1000 genomes]
rs8014296	0.87[CHB][hapmap]
rs8018674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8019539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8022985	1.00[ASN][1000 genomes]
rs874025	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs877561	0.86[CHB][hapmap]
rs962539	0.91[CHB][hapmap];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7145309	NRXN3	cis	cerebellum	SCAN
rs7145309	ADCK1	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78297800-78353600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr14:78306000-78356400	Weak transcription	Thymus	Thymus
3	chr14:78310400-78345000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr14:78314200-78348400	Weak transcription	Colon Smooth Muscle	Colon
5	chr14:78321400-78342800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr14:78321800-78348400	Weak transcription	Placenta	Placenta
7	chr14:78322000-78342600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr14:78322200-78353400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr14:78324000-78353600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr14:78324200-78354800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr14:78325000-78345000	Weak transcription	Brain Angular Gyrus	brain
12	chr14:78326600-78352800	Weak transcription	Esophagus	oesophagus
13	chr14:78327200-78348600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr14:78327800-78400600	Weak transcription	Colonic Mucosa	Colon
15	chr14:78328000-78353400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr14:78329000-78345000	Weak transcription	Brain Substantia Nigra	brain
17	chr14:78329000-78345800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr14:78329000-78347600	Weak transcription	Brain Anterior Caudate	brain
19	chr14:78329000-78348400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr14:78329200-78345400	Weak transcription	Right Ventricle	heart
21	chr14:78329400-78345200	Weak transcription	Brain Hippocampus Middle	brain
22	chr14:78333400-78348600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr14:78334600-78353400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr14:78335800-78348400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr14:78335800-78358600	Weak transcription	HSMMtube	muscle
26	chr14:78336400-78354200	Weak transcription	Fetal Intestine Large	intestine
27	chr14:78337200-78345400	Weak transcription	Left Ventricle	heart
28	chr14:78339000-78345400	Weak transcription	K562	blood
29	chr14:78339600-78353800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr14:78340000-78353400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr14:78340400-78353600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr14:78340600-78348200	Weak transcription	Fetal Muscle Leg	muscle
33	chr14:78340600-78353400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr14:78340600-78353400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr14:78340600-78353600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr14:78340600-78353600	Weak transcription	Dnd41	blood
37	chr14:78340800-78354200	Weak transcription	Primary B cells from cord blood	blood
38	chr14:78341000-78344800	Weak transcription	Pancreas	Pancrea
39	chr14:78341000-78349800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr14:78341400-78344800	Weak transcription	Gastric	stomach
41	chr14:78341800-78343200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
42	chr14:78342000-78342400	Enhancers	Fetal Heart	heart
43	chr14:78342000-78342600	ZNF genes & repeats	Spleen	Spleen
44	chr14:78342000-78342800	ZNF genes & repeats	Adipose Nuclei	Adipose
45	chr14:78342000-78342800	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr14:78342200-78342600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
47	chr14:78342200-78342800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
48	chr14:78342200-78343000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
49	chr14:78342200-78344600	Weak transcription	Liver	Liver
50	chr14:78342200-78346400	Strong transcription	Primary T cells from cord blood	blood

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