Variant report

Variant	rs3734504
Chromosome Location	chr6:2413792-2413793
allele	A/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	CEBPB	chr6:2413789-2414096	K562	blood:	n/a	chr6:2413967-2413978

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:2244221..2245990-chr6:2413292..2415770,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WRNIP1-2	chr6:2413014-2413825	NONHSAT106620

Variant related genes	Relation type
ENSG00000266252	TF binding region
ENSG00000112699	Chromatin interaction
ENSG00000250903	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11965611	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11968173	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12524370	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12529088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13191094	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13198172	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13200914	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13204171	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13214285	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13220248	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17536894	0.86[EUR][1000 genomes]
rs17608626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17609498	0.85[EUR][1000 genomes]
rs28360628	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34172338	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34610626	0.86[EUR][1000 genomes]
rs34854900	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34901328	0.86[EUR][1000 genomes]
rs34932214	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34996746	0.82[EUR][1000 genomes]
rs35182831	0.85[EUR][1000 genomes]
rs35590232	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35892674	0.86[EUR][1000 genomes]
rs35918040	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3734505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734507	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3823107	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4596531	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959175	0.82[EUR][1000 genomes]
rs4959176	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4959177	0.88[AMR][1000 genomes]
rs4959180	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4959181	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959182	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959654	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959658	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959661	0.82[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959662	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959665	0.83[AMR][1000 genomes]
rs55939357	0.81[EUR][1000 genomes]
rs56343276	0.86[EUR][1000 genomes]
rs59493792	0.86[EUR][1000 genomes]
rs62391186	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6902556	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6908555	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6911665	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71552124	0.85[EUR][1000 genomes]
rs7738954	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7755646	0.85[AMR][1000 genomes]
rs7773388	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9501836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503186	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503187	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503188	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503189	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9791368	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3734504	FOXQ1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2392400-2414400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr6:2396800-2415400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:2399800-2414000	Weak transcription	Fetal Stomach	stomach
4	chr6:2399800-2449200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:2401200-2417400	Weak transcription	Pancreas	Pancrea
6	chr6:2401200-2421000	Weak transcription	Fetal Intestine Large	intestine
7	chr6:2401400-2414000	Weak transcription	Lung	lung
8	chr6:2401400-2426200	Weak transcription	Aorta	Aorta
9	chr6:2401600-2413800	Weak transcription	Fetal Intestine Small	intestine
10	chr6:2402000-2415600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:2402200-2417400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:2402200-2449200	Weak transcription	Left Ventricle	heart
13	chr6:2404000-2415200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:2404400-2415400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:2404800-2414000	Weak transcription	Liver	Liver
16	chr6:2405000-2417800	Weak transcription	Primary T cells from cord blood	blood
17	chr6:2412000-2413800	Weak transcription	Ovary	ovary
18	chr6:2412400-2414000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr6:2412600-2413800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:2412800-2413800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:2412800-2413800	Enhancers	HUVEC	blood vessel
22	chr6:2412800-2413800	Flanking Active TSS	Osteobl	bone
23	chr6:2412800-2414800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:2413000-2413800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:2413000-2414200	Strong transcription	Adipose Nuclei	Adipose
26	chr6:2413600-2414200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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