Variant report

Variant	rs6858440
Chromosome Location	chr4:47917474-47917475
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	MAX	chr4:47915851-47917523	K562	blood:	n/a	n/a
3	MYC	chr4:47916447-47917478	MCF10A-Er-Src	breast:	n/a	n/a
4	SREBP1	chr4:47915452-47917966	GM12878	blood:	n/a	n/a
5	TBL1XR1	chr4:47916248-47917503	K562	blood:	n/a	n/a
6	MYC	chr4:47915385-47917613	K562	blood:	n/a	n/a
7	SIN3A	chr4:47915359-47917497	H1-hESC	embryonic stem cell:	n/a	n/a
8	MYC	chr4:47915409-47917556	K562	blood:	n/a	n/a

Variant related genes	Relation type
NFXL1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10002500	0.86[ASW][hapmap];0.80[LWK][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap]
rs10008818	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs10028155	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10049713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1012844	0.85[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs10517204	0.80[ASW][hapmap]
rs1062858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10805163	0.80[ASW][hapmap]
rs10938499	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10938500	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10938504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10938505	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10938506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12186152	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12504018	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12506632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12507439	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12510002	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12641871	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12651301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1371729	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1371731	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1396051	0.80[ASW][hapmap]
rs1440228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17463666	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17573709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1822030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1866689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1984713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2033893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289435	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2352470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2661513	0.95[YRI][hapmap]
rs28395298	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28412313	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28460483	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28573115	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28583602	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28636596	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3113881	0.86[YRI][hapmap]
rs321623	0.86[ASW][hapmap];0.82[YRI][hapmap]
rs4435717	0.83[EUR][1000 genomes]
rs4565052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56001837	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6447587	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6447589	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6811177	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6823184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6823698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6833758	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8180146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs978094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9994561	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9995122	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9997555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6858440	CNGA1	cis	cerebellum	SCAN
rs6858440	CNGA1	cis	Adipose Subcutaneous	GTEx
rs6858440	RP11-121C2.2	cis	Whole Blood	GTEx
rs6858440	TNFRSF1A	trans	lymphoblastoid	seeQTL
rs6858440	CNGA1	cis	Heart Left Ventricle	GTEx
rs6858440	CORIN	cis	Whole Blood	GTEx
rs6858440	CNGA1	cis	Muscle Skeletal	GTEx
rs6858440	NFXL1	cis	Whole Blood	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47914400-47917600	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr4:47914400-47917600	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:47915000-47917600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr4:47915200-47917600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:47915400-47917600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr4:47915600-47917600	Active TSS	Fetal Brain Female	brain
7	chr4:47915600-47917800	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr4:47915800-47917600	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr4:47916000-47917600	Active TSS	Thymus	Thymus
10	chr4:47916600-47917600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:47916800-47917800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr4:47916800-47917800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr4:47916800-47917800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:47916800-47917800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr4:47917000-47917600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:47917200-47917600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:47917200-47917600	Enhancers	Primary B cells from peripheral blood	blood
18	chr4:47917200-47917600	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr4:47917200-47917600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:47917200-47917600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:47917200-47917600	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr4:47917200-47917600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:47917200-47917600	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr4:47917200-47917600	Enhancers	Stomach Mucosa	stomach
25	chr4:47917200-47917600	Enhancers	Spleen	Spleen
26	chr4:47917200-47917600	Flanking Active TSS	HMEC	breast
27	chr4:47917200-47917600	Enhancers	NHLF	lung
28	chr4:47917200-47917800	Enhancers	Primary B cells from cord blood	blood
29	chr4:47917200-47917800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:47917200-47917800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr4:47917200-47917800	Enhancers	Hela-S3	cervix
32	chr4:47917400-47917600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:47917400-47917600	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr4:47917400-47917600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr4:47917400-47917600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:47917400-47917600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:47917400-47917600	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr4:47917400-47917600	Enhancers	Liver	Liver
39	chr4:47917400-47917600	Enhancers	Brain Angular Gyrus	brain
40	chr4:47917400-47917600	Enhancers	Brain Cingulate Gyrus	brain
41	chr4:47917400-47917600	Enhancers	Fetal Heart	heart
42	chr4:47917400-47917600	Enhancers	A549	lung
43	chr4:47917400-47917600	Flanking Active TSS	HepG2	liver
44	chr4:47917400-47917600	Enhancers	K562	blood
45	chr4:47917400-47917600	Flanking Active TSS	NH-A	brain
46	chr4:47917400-47917600	Flanking Active TSS	NHEK	skin
47	chr4:47917400-47917600	Enhancers	Osteobl	bone
48	chr4:47917400-47917800	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr4:47917400-47917800	Enhancers	Primary T cells from cord blood	blood
50	chr4:47917400-47917800	Enhancers	Primary T helper cells PMA-I stimulated	--

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