Variant report

Variant	rs2489185
Chromosome Location	chr1:92297986-92297987
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	FOS	chr1:92297946-92298017	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:92297787-92298075	MCF10A-Er-Src	breast:	n/a	chr1:92297908-92297916
3	FOS	chr1:92297983-92298155	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:92297943-92298055	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr1:92297857-92298133	HepG2	liver:	n/a	chr1:92298002-92298013
6	CEBPB	chr1:92297968-92298078	Hela-S3	cervix:	n/a	chr1:92298002-92298013

Variant related genes	Relation type
RN7SL653P	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1032255	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10874980	0.84[ASN][1000 genomes]
rs11165578	0.83[ASN][1000 genomes]
rs11799400	0.84[EUR][1000 genomes]
rs12027931	0.84[EUR][1000 genomes]
rs1352438	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1805109	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1805110	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1906586	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2046737	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2087300	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2129972	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2129973	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2256471	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2265863	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2391070	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2450926	0.83[EUR][1000 genomes]
rs2450927	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2489169	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2489170	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2489171	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2489176	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2489178	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2489184	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2489186	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2489192	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634019	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634020	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2634022	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634023	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634024	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634025	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634026	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634027	0.85[EUR][1000 genomes]
rs2634028	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634029	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634030	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634032	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2634033	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2634034	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2634036	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2799512	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2799514	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2799515	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2799516	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2799517	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2799521	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2799522	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2799523	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2799524	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2799525	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2799539	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2799547	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2810903	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs284141	0.84[EUR][1000 genomes]
rs284146	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284148	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284150	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284151	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284156	0.82[ASN][1000 genomes]
rs284157	0.82[ASN][1000 genomes]
rs284160	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs284161	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs284162	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs284163	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs284164	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3103332	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3103333	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs449960	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs717923	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7550856	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs901913	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs901914	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs901915	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs901917	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92293400-92298000	Enhancers	Fetal Heart	heart
2	chr1:92294600-92298200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:92294600-92298600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:92294800-92311600	Weak transcription	Gastric	stomach
5	chr1:92295600-92298000	Enhancers	NHLF	lung
6	chr1:92296200-92298200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:92296400-92298000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:92296400-92335800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:92296600-92298000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:92296600-92298200	Enhancers	Colon Smooth Muscle	Colon
11	chr1:92296600-92298200	Enhancers	Rectal Smooth Muscle	rectum
12	chr1:92296600-92298200	Enhancers	A549	lung
13	chr1:92296600-92298400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:92296800-92298600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:92296800-92299400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:92296800-92300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:92296800-92307400	Weak transcription	Lung	lung
18	chr1:92296800-92307800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:92296800-92309400	Weak transcription	Left Ventricle	heart
20	chr1:92296800-92311400	Weak transcription	Stomach Mucosa	stomach
21	chr1:92297000-92298000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:92297000-92300000	Weak transcription	Placenta	Placenta
23	chr1:92297000-92308000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:92297000-92310400	Weak transcription	Pancreas	Pancrea
25	chr1:92297000-92311000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:92297200-92298000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:92297200-92298000	Weak transcription	Fetal Stomach	stomach
28	chr1:92297200-92298200	Enhancers	Duodenum Mucosa	Duodenum
29	chr1:92297200-92299200	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:92297200-92300600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:92297200-92300600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:92297200-92300600	Weak transcription	Ovary	ovary
33	chr1:92297200-92300600	Weak transcription	Small Intestine	intestine
34	chr1:92297200-92300800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:92297200-92301600	Enhancers	HepG2	liver
36	chr1:92297200-92306600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:92297200-92308200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:92297200-92311800	Weak transcription	Fetal Intestine Large	intestine
39	chr1:92297200-92313600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:92297400-92298000	Enhancers	Stomach Smooth Muscle	stomach
41	chr1:92297400-92298200	Enhancers	Hela-S3	cervix
42	chr1:92297400-92304600	Weak transcription	NHDF-Ad	bronchial
43	chr1:92297600-92298000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:92297600-92298000	Weak transcription	Fetal Kidney	kidney
45	chr1:92297600-92298200	Enhancers	NHEK	skin
46	chr1:92297800-92298400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:92297800-92299400	Weak transcription	Fetal Lung	lung
48	chr1:92297800-92300400	Weak transcription	Liver	Liver
49	chr1:92297800-92310400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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