Variant report

Variant	rs6832334
Chromosome Location	chr4:47917730-47917731
allele	A/G
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	MAZ	chr4:47915811-47917764	IMR90	lung:	n/a	n/a
2	SREBP1	chr4:47915452-47917966	GM12878	blood:	n/a	n/a
3	NFYB	chr4:47917600-47917800	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
NFXL1	TF binding region

Extended variants
information (count: 116 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10002498	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020447	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025104	0.81[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs10030927	0.81[CEU][hapmap]
rs1036681	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461075	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805158	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10938498	0.81[EUR][1000 genomes]
rs10938508	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11732840	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946535	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506026	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647189	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13143926	0.87[ASN][1000 genomes]
rs1348023	0.89[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap]
rs1371728	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1440220	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs1440222	1.00[ASN][1000 genomes]
rs1440227	0.81[CEU][hapmap]
rs1507922	0.90[GIH][hapmap];0.85[TSI][hapmap]
rs1545200	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550444	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167692	0.89[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs1808853	0.88[EUR][1000 genomes]
rs1812964	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188900	1.00[ASN][1000 genomes]
rs1968542	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972883	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972884	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014934	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033894	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2033895	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053404	0.81[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs2119204	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119205	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2119207	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119208	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224801	0.87[ASN][1000 genomes]
rs2289433	0.81[CEU][hapmap];0.97[GIH][hapmap]
rs2352456	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352457	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352466	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2581496	1.00[ASN][1000 genomes]
rs28464733	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882950	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113877	1.00[ASN][1000 genomes]
rs3113879	1.00[ASN][1000 genomes]
rs3113880	0.87[ASN][1000 genomes]
rs321625	1.00[ASN][1000 genomes]
rs321639	0.89[ASN][1000 genomes]
rs321640	1.00[ASN][1000 genomes]
rs321641	0.87[ASN][1000 genomes]
rs321647	0.87[ASN][1000 genomes]
rs321649	0.87[ASN][1000 genomes]
rs3762858	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762859	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811761	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845160	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308343	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365692	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4507330	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529019	0.81[CEU][hapmap]
rs4694868	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694871	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694872	0.81[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs4694875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4694878	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695287	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695294	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4695296	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4695302	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695303	0.81[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs4695306	0.81[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs4695309	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695312	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695316	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6414687	0.81[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs6447586	0.81[CEU][hapmap]
rs6447593	0.85[CEU][hapmap]
rs6447596	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447599	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447602	0.84[EUR][1000 genomes]
rs6815975	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818556	0.81[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs6819506	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823572	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826909	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827508	0.88[CEU][hapmap]
rs6829073	0.92[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs6833320	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841271	0.89[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs6844286	0.81[CEU][hapmap]
rs6845451	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850142	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs707723	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668778	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670219	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671780	1.00[JPT][hapmap]
rs7672090	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690406	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690522	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690562	0.83[CEU][hapmap]
rs893861	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893863	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893864	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291317	0.81[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs9291318	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291319	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995022	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6832334	CNGA1	cis	Thyroid	GTEx
rs6832334	CNGA1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47915600-47917800	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr4:47916800-47917800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr4:47916800-47917800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr4:47916800-47917800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:47916800-47917800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr4:47917200-47917800	Enhancers	Primary B cells from cord blood	blood
7	chr4:47917200-47917800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:47917200-47917800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr4:47917200-47917800	Enhancers	Hela-S3	cervix
10	chr4:47917400-47917800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr4:47917400-47917800	Enhancers	Primary T cells from cord blood	blood
12	chr4:47917400-47917800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr4:47917400-47917800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:47917400-47917800	Enhancers	Fetal Intestine Large	intestine
15	chr4:47917400-47917800	Enhancers	Fetal Intestine Small	intestine
16	chr4:47917400-47917800	Enhancers	Dnd41	blood
17	chr4:47917400-47917800	Flanking Active TSS	GM12878-XiMat	blood
18	chr4:47917400-47917800	Enhancers	HUVEC	blood vessel
19	chr4:47917400-47918000	Enhancers	Duodenum Mucosa	Duodenum
20	chr4:47917600-47917800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr4:47917600-47917800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:47917600-47917800	Enhancers	Primary hematopoietic stem cells	blood
23	chr4:47917600-47917800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr4:47917600-47917800	Enhancers	HepG2	liver
25	chr4:47917600-47917800	Enhancers	HMEC	breast
26	chr4:47917600-47917800	Enhancers	NHEK	skin

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