Variant report

Variant	rs726743
Chromosome Location	chr6:5036667-5036668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1108040	0.82[ASN][1000 genomes]
rs1108041	0.85[ASN][1000 genomes]
rs11967778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11967814	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12200195	0.81[ASN][1000 genomes]
rs1627212	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17139235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1749155	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1771868	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1771873	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1771874	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1815673	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1815674	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1815675	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2002380	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2147705	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2764128	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2764131	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2764133	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2764140	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2764144	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2764147	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2764150	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2764153	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2764154	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2764170	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2764189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2793239	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2793246	0.92[EUR][1000 genomes]
rs2793252	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793253	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793254	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793256	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793257	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793258	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793259	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2793260	0.84[AFR][1000 genomes]
rs2985677	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2994695	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2994696	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4246072	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4281005	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57919800	0.90[AFR][1000 genomes]
rs62385148	0.81[ASN][1000 genomes]
rs62385159	0.81[ASN][1000 genomes]
rs62386470	0.81[ASN][1000 genomes]
rs707964	0.85[GIH][hapmap]
rs73365175	0.85[ASN][1000 genomes]
rs754334	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs811259	0.82[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs877229	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9378925	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
10	esv3407355	chr6:5034778-5037326	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
11	esv3446130	chr6:5034953-5037401	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
12	esv3381089	chr6:5036503-5040201	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs726743	FOXF2	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5027200-5047200	Weak transcription	Adipose Nuclei	Adipose
2	chr6:5031200-5042800	Weak transcription	Ovary	ovary
3	chr6:5031600-5042800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:5031800-5043800	Weak transcription	Spleen	Spleen
5	chr6:5032800-5037200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:5033400-5036800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:5033400-5046000	Weak transcription	Fetal Intestine Small	intestine
8	chr6:5033400-5048600	Weak transcription	Aorta	Aorta
9	chr6:5034400-5045200	Weak transcription	Fetal Stomach	stomach
10	chr6:5034800-5045600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:5034800-5047400	Weak transcription	Esophagus	oesophagus
12	chr6:5035000-5037600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:5035000-5047400	Weak transcription	Primary B cells from cord blood	blood
14	chr6:5035400-5037200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:5035400-5047800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:5035600-5036800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:5035800-5036800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:5035800-5042600	Weak transcription	Placenta	Placenta
19	chr6:5036000-5037200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr6:5036200-5036800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr6:5036200-5036800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr6:5036200-5037000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:5036200-5037000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:5036200-5037000	Enhancers	HSMM	muscle
25	chr6:5036200-5037200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr6:5036200-5037200	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr6:5036200-5037200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:5036200-5037200	Enhancers	NHEK	skin
29	chr6:5036400-5036800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr6:5036400-5036800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr6:5036400-5037000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr6:5036400-5037000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:5036400-5037000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:5036400-5037000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:5036400-5037000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:5036400-5037000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr6:5036400-5037000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:5036400-5037000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr6:5036400-5037000	Enhancers	A549	lung
40	chr6:5036400-5037000	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr6:5036400-5037200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:5036400-5037200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr6:5036400-5037200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:5036400-5037200	Enhancers	HepG2	liver
45	chr6:5036400-5037200	Enhancers	K562	blood
46	chr6:5036600-5036800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr6:5036600-5036800	Enhancers	Fetal Lung	lung
48	chr6:5036600-5037000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:5036600-5037000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:5036600-5037200	Enhancers	H1 Cell Line	embryonic stem cell

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