Variant report

Variant	rs14030
Chromosome Location	chr14:71956141-71956142
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	chr14:71956124..71958303-chr14:72214679..72216703,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIPA1L1-2	chr14:71955871-71956294	NONHSAT037636
2	lnc-SIPA1L1-2	chr14:71954578-71956420	NONHSAT037641

Extended variants
information (count: 184 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:182)

rs_ID	r²[population]
rs10135680	0.80[EUR][1000 genomes]
rs10138557	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10139519	0.91[CEU][hapmap]
rs1029570	0.82[EUR][1000 genomes]
rs10483836	0.84[EUR][1000 genomes]
rs11848785	0.88[EUR][1000 genomes]
rs12127	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12433040	0.82[EUR][1000 genomes]
rs12878989	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12879243	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12880188	0.95[CEU][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs12880291	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12880611	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12881643	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12881957	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12884929	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12885344	0.83[EUR][1000 genomes]
rs12887261	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12889866	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12891975	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12892512	0.84[EUR][1000 genomes]
rs12894016	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12894478	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12896900	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs12896986	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17178045	0.82[EUR][1000 genomes]
rs17178206	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17178234	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17178387	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17767386	0.82[EUR][1000 genomes]
rs17767392	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs17767398	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17767410	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs17767446	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17767499	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17767523	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17767553	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17767680	0.84[EUR][1000 genomes]
rs17767686	0.84[EUR][1000 genomes]
rs1859643	0.82[EUR][1000 genomes]
rs1981588	0.91[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1990241	0.83[EUR][1000 genomes]
rs2108049	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2108057	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs2108706	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs2108707	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2109276	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2190240	0.82[EUR][1000 genomes]
rs2214836	0.82[EUR][1000 genomes]
rs2332638	0.82[EUR][1000 genomes]
rs2332640	0.82[EUR][1000 genomes]
rs2332641	0.80[EUR][1000 genomes]
rs2877729	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28859432	0.80[EUR][1000 genomes]
rs33994051	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34011442	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34057981	0.84[EUR][1000 genomes]
rs34061264	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34169215	0.84[EUR][1000 genomes]
rs34176710	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34281405	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34281934	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34320622	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34347034	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34388001	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34454371	0.90[EUR][1000 genomes]
rs34469007	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34480562	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34524083	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34528013	0.82[EUR][1000 genomes]
rs34528131	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34533948	0.85[EUR][1000 genomes]
rs34649709	0.84[EUR][1000 genomes]
rs34674149	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs34725136	0.85[EUR][1000 genomes]
rs34746156	0.84[EUR][1000 genomes]
rs34748537	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34767050	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34873919	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34911660	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34957192	0.80[EUR][1000 genomes]
rs34991781	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34993988	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35051046	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35054229	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35094946	0.84[EUR][1000 genomes]
rs35122644	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35151594	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35231795	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35260692	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35415083	0.84[EUR][1000 genomes]
rs35468256	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35589413	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35609708	0.84[EUR][1000 genomes]
rs35613269	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35620527	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35621718	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35625243	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35680546	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35692397	0.82[EUR][1000 genomes]
rs35760654	0.84[EUR][1000 genomes]
rs35796129	0.85[EUR][1000 genomes]
rs35822724	0.86[EUR][1000 genomes]
rs35831373	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35854505	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35866366	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35971049	0.84[EUR][1000 genomes]
rs36052007	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36057816	0.82[EUR][1000 genomes]
rs36072220	0.85[EUR][1000 genomes]
rs36093218	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3784062	0.81[EUR][1000 genomes]
rs3784064	0.91[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs3784066	0.84[EUR][1000 genomes]
rs3825719	0.91[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs4453405	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4899394	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4899398	0.91[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4902938	0.84[EUR][1000 genomes]
rs55883127	0.84[EUR][1000 genomes]
rs56180634	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56363446	0.82[EUR][1000 genomes]
rs56407721	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61989367	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61989373	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61989374	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61989377	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61989379	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989382	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61989383	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61989386	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61991199	0.84[EUR][1000 genomes]
rs61991200	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61991201	0.84[EUR][1000 genomes]
rs61991202	0.85[EUR][1000 genomes]
rs61991203	0.82[EUR][1000 genomes]
rs61991204	0.82[EUR][1000 genomes]
rs61991205	0.83[EUR][1000 genomes]
rs61991213	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61991243	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61991246	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61991247	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61991248	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61991249	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61991250	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61991254	0.87[EUR][1000 genomes]
rs61991255	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6574016	0.82[EUR][1000 genomes]
rs66645707	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67489015	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs68073803	0.85[EUR][1000 genomes]
rs7140354	0.82[EUR][1000 genomes]
rs7140501	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7142180	0.82[EUR][1000 genomes]
rs7142214	0.90[EUR][1000 genomes]
rs7142343	0.91[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7144299	0.82[EUR][1000 genomes]
rs7144829	0.82[EUR][1000 genomes]
rs7145755	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7147434	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7147668	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7152674	0.84[EUR][1000 genomes]
rs7152842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7154841	0.82[EUR][1000 genomes]
rs7156313	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7156460	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7157241	0.84[EUR][1000 genomes]
rs722633	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs723966	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs725673	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72728427	0.86[EUR][1000 genomes]
rs757850	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8006300	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs8007068	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs8008605	0.82[EUR][1000 genomes]
rs8013161	0.88[EUR][1000 genomes]
rs8014349	0.82[EUR][1000 genomes]
rs8015644	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8017775	0.82[EUR][1000 genomes]
rs8019721	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9323561	0.82[EUR][1000 genomes]
rs9672060	0.96[CEU][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]

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	nsv498021	chr14:71874708-72128721	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3398985	chr14:71927884-72404676	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs14030	MAP3K9	cis	cerebellum	SCAN
rs14030	PCNX	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71929200-71964200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr14:71935400-71980400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr14:71939000-71959800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr14:71942000-71964200	Weak transcription	Hela-S3	cervix
5	chr14:71945800-71956200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr14:71945800-71956400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr14:71946000-71959800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr14:71946000-71963200	Weak transcription	Dnd41	blood
9	chr14:71946000-71995600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr14:71947000-71964600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr14:71948200-71958600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr14:71949200-71958600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:71950400-71958800	Weak transcription	Fetal Kidney	kidney
14	chr14:71950600-71958000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr14:71950800-71958200	Weak transcription	Ovary	ovary
16	chr14:71950800-71958600	Weak transcription	Lung	lung
17	chr14:71951000-71956200	Enhancers	Fetal Lung	lung
18	chr14:71952200-71962600	Weak transcription	Primary B cells from cord blood	blood
19	chr14:71953800-71956200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr14:71953800-71956200	Enhancers	Brain Cingulate Gyrus	brain
21	chr14:71953800-71956200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr14:71953800-71956200	Enhancers	Rectal Smooth Muscle	rectum
23	chr14:71953800-71956200	Enhancers	Stomach Mucosa	stomach
24	chr14:71953800-71956800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr14:71954000-71956200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr14:71954000-71956200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr14:71954000-71956200	Enhancers	Fetal Heart	heart
28	chr14:71954000-71956800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr14:71954200-71956200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr14:71954200-71956200	Enhancers	Brain Hippocampus Middle	brain
31	chr14:71954200-71956200	Enhancers	Fetal Stomach	stomach
32	chr14:71954200-71956800	Enhancers	Brain Substantia Nigra	brain
33	chr14:71954200-71959800	Weak transcription	Right Atrium	heart
34	chr14:71954400-71956200	Enhancers	NH-A	brain
35	chr14:71954400-71957200	Enhancers	NHDF-Ad	bronchial
36	chr14:71954400-71958600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr14:71954400-71960400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr14:71954400-71978200	Weak transcription	Primary T cells from cord blood	blood
39	chr14:71954600-71956200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr14:71954600-71956200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr14:71954800-71956800	Enhancers	Fetal Intestine Small	intestine
42	chr14:71954800-71958200	Weak transcription	Spleen	Spleen
43	chr14:71954800-71964200	Weak transcription	NHEK	skin
44	chr14:71955000-71956200	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr14:71955000-71958600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr14:71955000-71964000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr14:71955200-71956200	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr14:71955200-71956200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr14:71955200-71956200	Enhancers	Brain Angular Gyrus	brain
50	chr14:71955200-71956200	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links