Variant report

Variant	rs6426123
Chromosome Location	chr1:224624391-224624392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr1:224622177-224624682	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNIH3-2	chr1:224624195-224624607	NONHSAT009806

Variant related genes	Relation type
WDR26	TF binding region

Extended variants
information (count: 122 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10127813	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs10127953	0.89[EUR][1000 genomes]
rs10128058	0.89[EUR][1000 genomes]
rs10159333	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495219	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10753466	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753467	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753468	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10799569	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10799573	0.88[MEX][hapmap]
rs10799574	0.88[MEX][hapmap]
rs10916606	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10916607	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10916614	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916616	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916617	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10916619	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs11576835	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11577170	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11577183	0.88[EUR][1000 genomes]
rs11578709	0.88[EUR][1000 genomes]
rs11579952	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs11584057	0.85[EUR][1000 genomes]
rs11584247	0.88[EUR][1000 genomes]
rs11584638	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11584980	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11586729	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11588973	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11590658	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11800613	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11801436	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801645	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803414	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs11803981	0.89[EUR][1000 genomes]
rs11805973	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807763	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807942	0.88[EUR][1000 genomes]
rs11811053	0.85[EUR][1000 genomes]
rs12062871	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12731035	0.91[EUR][1000 genomes]
rs12731630	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12738799	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739486	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740255	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12742821	0.88[EUR][1000 genomes]
rs12742989	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12743200	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12745610	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12747286	0.96[EUR][1000 genomes]
rs12751161	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754832	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12755338	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12755816	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758302	0.94[EUR][1000 genomes]
rs12758579	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12759275	0.88[EUR][1000 genomes]
rs1539207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1544196	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848365	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503938	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17570292	0.86[EUR][1000 genomes]
rs2185684	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28434172	0.96[EUR][1000 genomes]
rs2897048	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs34791963	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35011635	0.99[EUR][1000 genomes]
rs35031726	0.89[EUR][1000 genomes]
rs35067427	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35169600	0.87[EUR][1000 genomes]
rs35277713	0.99[EUR][1000 genomes]
rs35303987	0.99[EUR][1000 genomes]
rs35341841	0.85[EUR][1000 genomes]
rs35365551	0.95[EUR][1000 genomes]
rs35571080	0.96[EUR][1000 genomes]
rs35767322	0.89[EUR][1000 genomes]
rs35804313	0.88[EUR][1000 genomes]
rs35915186	0.92[EUR][1000 genomes]
rs35972228	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36138926	0.89[EUR][1000 genomes]
rs4653585	1.00[CEU][hapmap]
rs4653587	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654037	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55730749	0.96[EUR][1000 genomes]
rs56223447	0.88[EUR][1000 genomes]
rs6426121	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426125	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6426126	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66467176	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6663522	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6671751	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs6672859	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6675858	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6691779	0.95[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs6693287	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6698343	0.86[EUR][1000 genomes]
rs6701145	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs67065875	0.89[EUR][1000 genomes]
rs68037178	0.87[EUR][1000 genomes]
rs71644786	0.90[EUR][1000 genomes]
rs7365151	0.96[EUR][1000 genomes]
rs7512431	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513208	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs7514284	0.89[ASW][hapmap];0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514575	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517754	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7518109	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519734	0.89[EUR][1000 genomes]
rs7522956	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527044	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529067	0.95[CEU][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7529310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867362	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885606	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970697	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1013149	chr1:224605943-224646382	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv535312	chr1:224605943-224646382	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6426123	CNIH4	cis	Muscle Skeletal	GTEx
rs6426123	CNIH4	cis	Heart Left Ventricle	GTEx
rs6426123	CNIH4	cis	parietal	SCAN
rs6426123	CNIH4	cis	Esophagus Muscularis	GTEx
rs6426123	CNIH4	cis	Thyroid	GTEx
rs6426123	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs6426123	CNIH4	cis	Esophagus Mucosa	GTEx
rs6426123	CNIH4	cis	Nerve Tibial	GTEx
rs6426123	CNIH4	cis	Stomach	GTEx
rs6426123	CNIH4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224623200-224624800	Flanking Active TSS	GM12878-XiMat	blood
2	chr1:224623200-224626200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:224623200-224634800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:224623200-224644400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:224623400-224624400	Enhancers	Fetal Kidney	kidney
6	chr1:224623400-224624400	Active TSS	K562	blood
7	chr1:224623400-224624600	Weak transcription	Esophagus	oesophagus
8	chr1:224623400-224624600	Weak transcription	Thymus	Thymus
9	chr1:224623400-224624800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:224623400-224624800	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr1:224623400-224624800	Enhancers	Fetal Lung	lung
12	chr1:224623400-224625000	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr1:224623400-224625200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr1:224623400-224626400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:224623400-224626800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:224623400-224626800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:224623400-224628200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:224623400-224631600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:224623400-224633400	Weak transcription	Gastric	stomach
20	chr1:224623400-224634600	Weak transcription	Lung	lung
21	chr1:224623400-224634800	Weak transcription	Aorta	Aorta
22	chr1:224623400-224634800	Weak transcription	Left Ventricle	heart
23	chr1:224623400-224634800	Weak transcription	Ovary	ovary
24	chr1:224623400-224634800	Weak transcription	Right Atrium	heart
25	chr1:224623400-224638000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:224623400-224641000	Weak transcription	Fetal Intestine Large	intestine
27	chr1:224623400-224643000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:224623400-224644600	Weak transcription	Right Ventricle	heart
29	chr1:224623600-224624400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:224623600-224624600	Enhancers	NH-A	brain
31	chr1:224623600-224624800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr1:224623600-224624800	Enhancers	Small Intestine	intestine
33	chr1:224623600-224625200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr1:224623600-224625200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr1:224623600-224625400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:224623600-224626800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:224623600-224627800	Weak transcription	Fetal Brain Female	brain
38	chr1:224623600-224627800	Weak transcription	Fetal Stomach	stomach
39	chr1:224623600-224628000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:224623600-224628800	Weak transcription	Brain Germinal Matrix	brain
41	chr1:224623600-224629800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:224623600-224630400	Weak transcription	Fetal Brain Male	brain
43	chr1:224623600-224635000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:224623600-224635600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:224623600-224636200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:224623600-224637400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:224623600-224642200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:224623600-224644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:224623600-224644600	Weak transcription	Brain Substantia Nigra	brain
50	chr1:224623800-224624600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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