Variant report

Variant	rs1250022
Chromosome Location	chr9:117878334-117878335
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	EP300	chr9:117878243-117878577	SK-N-SH_RA	brain:	n/a	n/a
2	CEBPB	chr9:117878134-117878689	HCT-116	colon:	n/a	n/a
3	TAF1	chr9:117878250-117878558	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr9:117858058-117881674	U87	brain:	n/a	n/a
5	POLR2A	chr9:117877891-117881556	U87	brain:	n/a	n/a
6	GATA3	chr9:117876789-117879555	SK-N-SH	brain:	n/a	chr9:117878767-117878775
7	CEBPB	chr9:117877946-117878565	IMR90	lung:	n/a	n/a
8	POLR2A	chr9:117878273-117878509	SK-N-SH	brain:	n/a	n/a
9	FOS	chr9:117876905-117878643	MCF10A-Er-Src	breast:	n/a	chr9:117877962-117877973 chr9:117877960-117877970 chr9:117877960-117877970 chr9:117877961-117877969 chr9:117877960-117877970 chr9:117877960-117877970
10	POLR2A	chr9:117877249-117881760	IMR90	lung:	n/a	n/a
11	TCF12	chr9:117876852-117879384	SK-N-SH	brain:	n/a	chr9:117876898-117876905
12	E2F4	chr9:117878296-117878602	MCF10A-Er-Src	breast:	n/a	n/a
13	CEBPB	chr9:117878242-117878586	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr9:117877221-117881586	U87	brain:	n/a	n/a
15	MAX	chr9:117878245-117878880	SK-N-SH	brain:	n/a	n/a
16	CEBPB	chr9:117878149-117878495	A549	lung:	n/a	n/a
17	PBX3	chr9:117878210-117879371	SK-N-SH	brain:	n/a	n/a
18	FOSL2	chr9:117877862-117878761	SK-N-SH	brain:	n/a	chr9:117877962-117877973 chr9:117877960-117877970 chr9:117877960-117877970 chr9:117877961-117877969 chr9:117877960-117877970 chr9:117877960-117877970
19	CEBPB	chr9:117878052-117878665	A549	lung:	n/a	n/a
20	CEBPB	chr9:117878122-117878630	ECC-1	luminal epithelium:	n/a	n/a
21	MYC	chr9:117878201-117878604	MCF10A-Er-Src	breast:	n/a	n/a
22	GATA3	chr9:117878154-117878757	SK-N-SH	brain:	n/a	n/a
23	MYC	chr9:117878227-117878512	MCF10A-Er-Src	breast:	n/a	n/a
24	EP300	chr9:117878220-117878561	SK-N-SH_RA	brain:	n/a	n/a
25	POLR2A	chr9:117877960-117879114	MCF10A-Er-Src	breast:	n/a	n/a
26	STAT3	chr9:117877582-117878608	MCF10A-Er-Src	breast:	n/a	chr9:117878450-117878462
27	RCOR1	chr9:117877222-117879859	IMR90	lung:	n/a	n/a
28	EP300	chr9:117877875-117879433	SK-N-SH	brain:	n/a	chr9:117879156-117879172
29	CEBPB	chr9:117878196-117878550	A549	lung:	n/a	n/a
30	FOSL2	chr9:117877736-117878627	SK-N-SH	brain:	n/a	chr9:117877962-117877973 chr9:117877960-117877970 chr9:117877960-117877970 chr9:117877961-117877969 chr9:117877960-117877970 chr9:117877960-117877970
31	JUND	chr9:117876669-117878747	SK-N-SH	brain:	n/a	chr9:117877962-117877973 chr9:117877960-117877970 chr9:117877960-117877970 chr9:117877961-117877969 chr9:117877960-117877970 chr9:117877960-117877970
32	TCF12	chr9:117876174-117879494	SK-N-SH	brain:	n/a	chr9:117876898-117876905
33	FOSL1	chr9:117878064-117878614	HCT-116	colon:	n/a	n/a
34	POLR2A	chr9:117878302-117878607	MCF10A-Er-Src	breast:	n/a	n/a
35	STAT3	chr9:117878173-117878601	MCF10A-Er-Src	breast:	n/a	chr9:117878450-117878462
36	JUND	chr9:117877706-117878731	SK-N-SH	brain:	n/a	chr9:117877962-117877973 chr9:117877960-117877970 chr9:117877960-117877970 chr9:117877961-117877969 chr9:117877960-117877970 chr9:117877960-117877970
37	FOS	chr9:117877790-117878768	MCF10A-Er-Src	breast:	n/a	chr9:117877962-117877973 chr9:117877960-117877970 chr9:117877960-117877970 chr9:117877961-117877969 chr9:117877960-117877970 chr9:117877960-117877970
38	STAT3	chr9:117878125-117878616	MCF10A-Er-Src	breast:	n/a	chr9:117878450-117878462
39	POLR2A	chr9:117876849-117879682	SK-N-SH	brain:	n/a	n/a
40	CEBPB	chr9:117878189-117878536	Hela-S3	cervix:	n/a	n/a
41	CEBPB	chr9:117877994-117878723	HCT-116	colon:	n/a	n/a
42	FOS	chr9:117877810-117878660	MCF10A-Er-Src	breast:	n/a	chr9:117877962-117877973 chr9:117877960-117877970 chr9:117877960-117877970 chr9:117877961-117877969 chr9:117877960-117877970 chr9:117877960-117877970
43	FOS	chr9:117877876-117878608	MCF10A-Er-Src	breast:	n/a	chr9:117877962-117877973 chr9:117877960-117877970 chr9:117877960-117877970 chr9:117877961-117877969 chr9:117877960-117877970 chr9:117877960-117877970
44	POLR2A	chr9:117863693-117881740	U87	brain:	n/a	n/a
45	EP300	chr9:117878224-117878517	Hela-S3	cervix:	n/a	n/a
46	PBX3	chr9:117877895-117878706	SK-N-SH	brain:	n/a	n/a
47	STAT3	chr9:117877575-117878704	MCF10A-Er-Src	breast:	n/a	chr9:117878450-117878462
48	FOSL2	chr9:117877894-117878654	A549	lung:	n/a	chr9:117877962-117877973 chr9:117877960-117877970 chr9:117877960-117877970 chr9:117877961-117877969 chr9:117877960-117877970 chr9:117877960-117877970
49	NFIC	chr9:117876700-117879564	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10982535	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1250019	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1250021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1250027	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1330355	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1330356	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1511	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1755639	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1755646	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1757106	0.96[CEU][hapmap]
rs1757107	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1819419	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1929395	0.82[JPT][hapmap]
rs2183701	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2274836	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2480930	0.80[AMR][1000 genomes]
rs2480932	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2480933	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789867	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3789868	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs769331	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs881496	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs944227	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]

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	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr9:117869200-117878400	Weak transcription	Fetal Lung	lung
2	chr9:117870400-117879000	Weak transcription	Esophagus	oesophagus
3	chr9:117875400-117879000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:117876000-117879400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:117876400-117880200	Enhancers	Hela-S3	cervix
6	chr9:117876600-117878600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:117876600-117879000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
8	chr9:117876800-117879000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr9:117876800-117879200	Enhancers	HSMM	muscle
10	chr9:117877000-117878400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:117877000-117879400	Flanking Active TSS	NH-A	brain
12	chr9:117877200-117881400	Active TSS	Fetal Kidney	kidney
13	chr9:117877400-117878400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
14	chr9:117877400-117878600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:117877400-117879400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:117877400-117879800	Flanking Active TSS	Osteobl	bone
17	chr9:117877600-117878400	Enhancers	Fetal Muscle Leg	muscle
18	chr9:117877600-117878600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
19	chr9:117877600-117879000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr9:117877600-117879800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:117877600-117880200	Enhancers	Placenta Amnion	Placenta Amnion
22	chr9:117877600-117881600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
23	chr9:117877800-117878600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:117877800-117878600	Weak transcription	HSMMtube	muscle
25	chr9:117877800-117878800	Weak transcription	Aorta	Aorta
26	chr9:117877800-117879200	Flanking Active TSS	NHDF-Ad	bronchial
27	chr9:117877800-117879600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
28	chr9:117877800-117880000	Active TSS	Fetal Brain Female	brain
29	chr9:117878000-117878400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr9:117878000-117878400	Enhancers	HMEC	breast
31	chr9:117878000-117880200	Active TSS	Stomach Smooth Muscle	stomach
32	chr9:117878000-117881600	Active TSS	Colon Smooth Muscle	Colon
33	chr9:117878200-117878400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr9:117878200-117878400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:117878200-117878400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:117878200-117878400	Flanking Active TSS	NHEK	skin
37	chr9:117878200-117878600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:117878200-117878600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:117878200-117878600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr9:117878200-117878600	Flanking Active TSS	Fetal Stomach	stomach
41	chr9:117878200-117878800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:117878200-117878800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
43	chr9:117878200-117880200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:117878200-117880400	Active TSS	Rectal Smooth Muscle	rectum
45	chr9:117878200-117880800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:117878200-117881000	Active TSS	NHLF	lung
47	chr9:117878200-117881400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:117878200-117881600	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr9:117878200-117881600	Active TSS	Duodenum Smooth Muscle	Duodenum

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