Variant report

Variant	rs11809665
Chromosome Location	chr1:186121251-186121252
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	GATA3	chr1:186121207-186122708	SK-N-SH	brain:	n/a	chr1:186122203-186122212 chr1:186121444-186121453 chr1:186121445-186121462
2	FOXM1	chr1:186121209-186122272	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr1:186121189-186122676	SK-N-SH	brain:	n/a	n/a
4	JUND	chr1:186121176-186122474	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr1:186121190-186122728	SK-N-SH	brain:	n/a	chr1:186122203-186122212 chr1:186121444-186121453 chr1:186121445-186121462
6	EP300	chr1:186121182-186122656	SK-N-SH	brain:	n/a	chr1:186121691-186121705
7	EP300	chr1:186121251-186121672	SK-N-SH_RA	brain:	n/a	n/a
8	GATA3	chr1:186121082-186123130	MCF-7	breast:	n/a	chr1:186122203-186122212 chr1:186121444-186121453 chr1:186121445-186121462
9	GATA3	chr1:186121249-186122866	MCF-7	breast:	n/a	chr1:186122203-186122212 chr1:186121444-186121453 chr1:186121445-186121462
10	SIN3AK20	chr1:186121240-186122915	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:186116473..186118652-chr1:186120353..186121946,2	MCF-7	breast:
2	chr1:186084110..186085893-chr1:186120570..186122700,2	MCF-7	breast:
3	chr1:186114622..186118208-chr1:186119499..186122583,5	MCF-7	breast:
4	chr1:186104914..186107979-chr1:186120191..186122595,3	MCF-7	breast:
5	chr1:185895832..185898136-chr1:186120386..186122778,2	MCF-7	breast:

Variant related genes	Relation type
HMCN1	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10489752	1.00[EUR][1000 genomes]
rs11808677	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11811575	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322376	0.83[AFR][1000 genomes]
rs16824945	0.94[EUR][1000 genomes]
rs16825022	0.89[EUR][1000 genomes]
rs16825024	0.89[EUR][1000 genomes]
rs4110541	0.83[AFR][1000 genomes]
rs41317507	1.00[EUR][1000 genomes]
rs55700344	1.00[ASN][1000 genomes]
rs58758627	1.00[EUR][1000 genomes]
rs59091582	1.00[EUR][1000 genomes]
rs59379268	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61831325	1.00[ASN][1000 genomes]
rs6658106	1.00[EUR][1000 genomes]
rs6672327	1.00[EUR][1000 genomes]
rs6673945	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72707450	0.94[EUR][1000 genomes]
rs72707466	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72707470	1.00[EUR][1000 genomes]
rs7527214	1.00[EUR][1000 genomes]
rs7552194	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	esv3424090	chr1:185679718-186270877	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186046400-186135200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:186073000-186121400	Weak transcription	NH-A	brain
3	chr1:186080400-186121400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:186109000-186121400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:186109200-186124600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:186109800-186121400	Weak transcription	NHDF-Ad	bronchial
7	chr1:186109800-186121600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:186112600-186122000	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:186113200-186124200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:186113800-186135800	Weak transcription	Ovary	ovary
11	chr1:186114000-186123200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:186114600-186160800	Weak transcription	Fetal Kidney	kidney
13	chr1:186115400-186135400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:186116000-186121800	Weak transcription	Left Ventricle	heart
15	chr1:186116400-186122800	Weak transcription	Adipose Nuclei	Adipose
16	chr1:186116400-186135400	Weak transcription	Aorta	Aorta
17	chr1:186116600-186135400	Weak transcription	Lung	lung
18	chr1:186117200-186135800	Weak transcription	Fetal Lung	lung
19	chr1:186120000-186135200	Weak transcription	Liver	Liver
20	chr1:186120200-186124600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:186120800-186123400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:186120800-186125800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:186121000-186121600	Enhancers	Placenta Amnion	Placenta Amnion
24	chr1:186121000-186122200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:186121200-186121400	Enhancers	Brain Substantia Nigra	brain
26	chr1:186121200-186121600	Enhancers	HMEC	breast
27	chr1:186121200-186122000	Enhancers	Brain Anterior Caudate	brain
28	chr1:186121200-186122000	Enhancers	Brain Hippocampus Middle	brain
29	chr1:186121200-186122200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:186121200-186122200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:186121200-186122200	Enhancers	NHLF	lung
32	chr1:186121200-186122200	Enhancers	Osteobl	bone
33	chr1:186121200-186122600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:186121200-186123000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:186121200-186123000	Enhancers	Hela-S3	cervix
36	chr1:186121200-186123200	Enhancers	NHEK	skin

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