Variant report

Variant	rs12224041
Chromosome Location	chr11:119999275-119999276
allele	A/G
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	RCOR1	chr11:119999253-120000037	Hela-S3	cervix:	n/a	n/a
2	FOS	chr11:119999211-119999962	MCF10A-Er-Src	breast:	n/a	n/a
3	FOXA1	chr11:119999178-119999877	T-47D	breast:	n/a	n/a
4	GATA3	chr11:119998961-119999861	T-47D	breast:	n/a	chr11:119999482-119999499
5	POLR2A	chr11:119999200-120000342	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:119999072-120000644	MCF10A-Er-Src	breast:	n/a	n/a
7	MXI1	chr11:119999221-120000114	Hela-S3	cervix:	n/a	n/a
8	SMC3	chr11:119999242-119999938	Hela-S3	cervix:	n/a	n/a
9	SMARCC1	chr11:119998967-120000301	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:119992602..119994710-chr11:119998240..120000665,2	MCF-7	breast:
2	chr11:119993537..119997499-chr11:119998076..120003019,6	K562	blood:
3	chr11:119999095..120001127-chr11:120038214..120040210,2	MCF-7	breast:
4	chr11:119995303..119997544-chr11:119999140..120002182,3	MCF-7	breast:

Variant related genes	Relation type
TRIM29	TF binding region
ENSG00000176984	Chromatin interaction
ENSG00000137699	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10790369	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10892544	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10892545	0.84[AMR][1000 genomes]
rs11217699	0.91[ASN][1000 genomes]
rs11217701	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11217702	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217705	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217706	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217707	0.89[AMR][1000 genomes]
rs11217708	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217710	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217711	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217713	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217715	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217716	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217718	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217719	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217720	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217721	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217722	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217723	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217724	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217725	1.00[EUR][1000 genomes]
rs11217726	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217727	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217728	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217729	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217730	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217731	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217732	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217733	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217734	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217735	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217736	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217737	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217738	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217739	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217740	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217741	1.00[EUR][1000 genomes]
rs11217742	1.00[EUR][1000 genomes]
rs11217743	1.00[EUR][1000 genomes]
rs11217744	1.00[EUR][1000 genomes]
rs11217745	0.84[AMR][1000 genomes]
rs11217746	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217748	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217749	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217750	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217751	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217753	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217754	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11535714	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12049837	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12224472	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12225418	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12274981	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12281157	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12283165	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12291620	0.84[AMR][1000 genomes]
rs12417084	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12417094	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12417234	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12418352	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12419511	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12419830	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12419976	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12419985	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12420985	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12421218	0.89[AMR][1000 genomes]
rs12422179	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34981150	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3740728	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3740729	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3740730	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3740731	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3781667	0.91[ASN][1000 genomes]
rs3781668	0.91[ASN][1000 genomes]
rs3781669	0.91[ASN][1000 genomes]
rs3824881	0.81[ASN][1000 genomes]
rs3824882	0.81[ASN][1000 genomes]
rs679074	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7118957	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7119349	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7119458	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1050132	chr11:119976310-120010437	Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119993400-119999800	Weak transcription	Fetal Thymus	thymus
2	chr11:119993400-120000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:119993800-120001800	Weak transcription	Pancreas	Pancrea
4	chr11:119995200-120000200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:119997600-120003200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
6	chr11:119998000-120000200	Genic enhancers	Esophagus	oesophagus
7	chr11:119998600-120000400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr11:119998600-120000800	Enhancers	Rectal Smooth Muscle	rectum
9	chr11:119998600-120001200	Enhancers	Colon Smooth Muscle	Colon
10	chr11:119998800-119999400	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr11:119998800-119999800	Enhancers	Colonic Mucosa	Colon
12	chr11:119998800-120000200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:119998800-120000200	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr11:119998800-120000400	Enhancers	Duodenum Mucosa	Duodenum
15	chr11:119998800-120000400	Enhancers	Stomach Mucosa	stomach
16	chr11:119998800-120000600	Enhancers	Fetal Intestine Large	intestine
17	chr11:119998800-120000800	Enhancers	Fetal Intestine Small	intestine
18	chr11:119999000-119999400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:119999000-119999400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr11:119999000-119999600	Flanking Active TSS	Hela-S3	cervix
21	chr11:119999000-119999600	Flanking Active TSS	HMEC	breast
22	chr11:119999000-119999800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:119999000-120000000	Enhancers	Adipose Nuclei	Adipose
24	chr11:119999000-120000600	Transcr. at gene 5' and 3'	NHEK	skin
25	chr11:119999000-120001400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:119999000-120001600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr11:119999000-120006400	Enhancers	Placenta	Placenta
28	chr11:119999200-119999600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:119999200-119999600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:119999200-119999600	Bivalent Enhancer	Fetal Stomach	stomach
31	chr11:119999200-119999800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr11:119999200-120000000	Bivalent Enhancer	Fetal Muscle Leg	muscle

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