Variant report

Variant	rs12726500
Chromosome Location	chr1:92296222-92296223
allele	A/C
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	CTCF	chr1:92296180-92296330	NHLF	lung:	n/a	n/a
2	EP300	chr1:92295786-92296661	HepG2	liver:	n/a	chr1:92296307-92296316
3	MAX	chr1:92295770-92296371	Hela-S3	cervix:	n/a	n/a
4	MAX	chr1:92295835-92296321	HepG2	liver:	n/a	n/a
5	SP1	chr1:92295665-92296239	A549	lung:	n/a	n/a
6	CTCF	chr1:92296220-92296370	GM12869	blood:	n/a	n/a
7	TBP	chr1:92295730-92296630	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:92295625-92296315	MCF10A-Er-Src	breast:	n/a	n/a
9	TFAP2A	chr1:92295716-92296222	Hela-S3	cervix:	n/a	chr1:92295980-92295990 chr1:92295980-92295990 chr1:92295864-92295875 chr1:92295980-92295990 chr1:92295980-92295990
10	TCF7L2	chr1:92295741-92297496	Hela-S3	cervix:	n/a	chr1:92297269-92297278
11	POLR2A	chr1:92295590-92297246	HepG2	liver:	n/a	n/a
12	RAD21	chr1:92295738-92296288	IMR90	lung:	n/a	n/a
13	POLR2A	chr1:92295660-92296237	MCF10A-Er-Src	breast:	n/a	n/a
14	RCOR1	chr1:92295319-92297229	IMR90	lung:	n/a	n/a
15	CTCF	chr1:92295491-92296316	A549	lung:	n/a	n/a
16	CHD2	chr1:92295810-92296347	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:92296078-92296265	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:92295773-92296397	HepG2	liver:	n/a	n/a
19	TFAP2C	chr1:92295647-92296345	Hela-S3	cervix:	n/a	n/a
20	MXI1	chr1:92295795-92296268	HepG2	liver:	n/a	n/a
21	RFX5	chr1:92296066-92296358	HepG2	liver:	n/a	chr1:92296099-92296114
22	RCOR1	chr1:92295844-92296595	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RN7SL653P	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10493857	0.82[CEU][hapmap]
rs10875030	0.82[CEU][hapmap]
rs11165556	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165595	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165637	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165679	0.82[CEU][hapmap]
rs11590254	0.86[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap]
rs1192524	0.82[CEU][hapmap]
rs1192528	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1192529	0.93[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12043241	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127774	0.82[CEU][hapmap]
rs12569180	0.82[CEU][hapmap]
rs17516329	0.86[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap]
rs17881430	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs2489188	0.82[MEX][hapmap]
rs2810904	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs284139	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs284140	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs284142	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs284143	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs284144	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs284147	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284149	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284152	0.89[CHB][hapmap];0.84[JPT][hapmap];0.88[YRI][hapmap]
rs284153	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284154	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs284159	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284167	0.81[EUR][1000 genomes]
rs416624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656018	0.82[CEU][hapmap]
rs7555476	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555548	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9661103	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv546819	chr1:92256626-92558583	Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv546820	chr1:92273644-92558583	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
22	nsv1007270	chr1:92289298-92598800	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12726500	GFI1	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92291600-92296600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr1:92292400-92297000	Enhancers	Placenta	Placenta
3	chr1:92293200-92296800	Enhancers	Right Atrium	heart
4	chr1:92293200-92297000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:92293400-92296400	Enhancers	Duodenum Mucosa	Duodenum
6	chr1:92293400-92296800	Enhancers	Esophagus	oesophagus
7	chr1:92293400-92296800	Enhancers	Left Ventricle	heart
8	chr1:92293400-92297200	Enhancers	Fetal Muscle Leg	muscle
9	chr1:92293400-92297600	Enhancers	Fetal Kidney	kidney
10	chr1:92293400-92298000	Enhancers	Fetal Heart	heart
11	chr1:92293600-92297000	Enhancers	Psoas Muscle	Psoas
12	chr1:92294000-92296800	Enhancers	Fetal Muscle Trunk	muscle
13	chr1:92294000-92296800	Enhancers	Spleen	Spleen
14	chr1:92294000-92297000	Enhancers	Right Ventricle	heart
15	chr1:92294200-92296800	Enhancers	Lung	lung
16	chr1:92294200-92297200	Enhancers	Ovary	ovary
17	chr1:92294200-92297800	Enhancers	Liver	Liver
18	chr1:92294400-92296400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr1:92294600-92298200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:92294600-92298600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:92294800-92297000	Enhancers	Pancreas	Pancrea
22	chr1:92294800-92311600	Weak transcription	Gastric	stomach
23	chr1:92295000-92296400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:92295200-92296600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:92295200-92297600	Weak transcription	NHEK	skin
26	chr1:92295400-92296800	Enhancers	Stomach Mucosa	stomach
27	chr1:92295400-92297000	Enhancers	Osteobl	bone
28	chr1:92295400-92297200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:92295400-92297200	Enhancers	Fetal Intestine Large	intestine
30	chr1:92295400-92297200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr1:92295400-92297400	Enhancers	Brain Hippocampus Middle	brain
32	chr1:92295400-92297400	Enhancers	GM12878-XiMat	blood
33	chr1:92295400-92297400	Genic enhancers	NHDF-Ad	bronchial
34	chr1:92295600-92296600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr1:92295600-92296600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:92295600-92296800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:92295600-92296800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:92295600-92296800	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr1:92295600-92296800	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr1:92295600-92297000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:92295600-92297000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:92295600-92297200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:92295600-92297200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:92295600-92297200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr1:92295600-92297200	Enhancers	Fetal Intestine Small	intestine
46	chr1:92295600-92297200	Flanking Active TSS	HepG2	liver
47	chr1:92295600-92297800	Enhancers	Fetal Lung	lung
48	chr1:92295600-92298000	Enhancers	NHLF	lung
49	chr1:92295800-92296400	Enhancers	Primary T cells from cord blood	blood
50	chr1:92295800-92296400	Enhancers	Brain Germinal Matrix	brain

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