Variant report

Variant	rs74086446
Chromosome Location	chr12:48372880-48372881
allele	C/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	ZNF263	chr12:48372682-48373169	HEK293-T-REx	kidney:	n/a	chr12:48372793-48372814 chr12:48372804-48372813

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48366493..48369414-chr12:48372046..48373592,2	K562	blood:
2	chr12:48372717..48377052-chr12:48391617..48394178,3	MCF-7	breast:

Variant related genes	Relation type
COL2A1	TF binding region
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10467100	1.00[EUR][1000 genomes]
rs11168264	1.00[EUR][1000 genomes]
rs11168288	1.00[EUR][1000 genomes]
rs11168290	1.00[EUR][1000 genomes]
rs11168368	1.00[EUR][1000 genomes]
rs11574002	1.00[EUR][1000 genomes]
rs11574060	1.00[EUR][1000 genomes]
rs11830088	1.00[EUR][1000 genomes]
rs11833896	1.00[EUR][1000 genomes]
rs11835282	1.00[EUR][1000 genomes]
rs11835720	1.00[EUR][1000 genomes]
rs11836542	1.00[EUR][1000 genomes]
rs11838217	1.00[EUR][1000 genomes]
rs12297117	1.00[EUR][1000 genomes]
rs1793947	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34116679	1.00[EUR][1000 genomes]
rs34120080	1.00[EUR][1000 genomes]
rs34698661	1.00[EUR][1000 genomes]
rs35445616	1.00[EUR][1000 genomes]
rs35902603	1.00[EUR][1000 genomes]
rs41272027	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41272035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41272745	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41272751	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41272757	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41272761	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56265470	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56387272	0.85[AFR][1000 genomes]
rs57444859	0.85[AFR][1000 genomes]
rs57550917	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57783574	1.00[EUR][1000 genomes]
rs58279970	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58431786	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58573495	1.00[EUR][1000 genomes]
rs58783688	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59339937	1.00[EUR][1000 genomes]
rs60556433	1.00[EUR][1000 genomes]
rs60894356	1.00[EUR][1000 genomes]
rs7316602	1.00[EUR][1000 genomes]
rs73297147	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73297150	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73297159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73297161	0.87[AFR][1000 genomes]
rs73297163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74085221	1.00[EUR][1000 genomes]
rs74086449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088715	1.00[EUR][1000 genomes]
rs74088779	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7954412	1.00[EUR][1000 genomes]
rs7967673	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv525456	chr12:48366449-48376969	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv558789	chr12:48368541-48376869	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48358400-48373000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:48358600-48381400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:48363400-48374800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:48363400-48375000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr12:48363400-48375000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr12:48363400-48383000	Weak transcription	Spleen	Spleen
8	chr12:48364400-48381200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:48365200-48381600	Weak transcription	Right Atrium	heart
10	chr12:48365400-48381000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:48366200-48381200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:48366200-48381400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:48366200-48381600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:48366600-48375200	Weak transcription	Gastric	stomach
15	chr12:48366800-48374800	Weak transcription	HepG2	liver
16	chr12:48368200-48373800	Weak transcription	Fetal Intestine Large	intestine
17	chr12:48370400-48374800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:48372400-48378400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:48372600-48374000	Weak transcription	Fetal Intestine Small	intestine
20	chr12:48372600-48374200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:48372800-48373200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin

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