Variant report

Variant	rs185053
Chromosome Location	chr16:75510212-75510213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:75495533..75500726-chr16:75509549..75515784,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GABARAPL2-1	chr16:75509794-75510218	ENSG00000203472.3

Variant related genes	Relation type
ENSG00000166822	Chromatin interaction
ENSG00000261717	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1540	0.89[ASN][1000 genomes]
rs2242405	0.89[ASN][1000 genomes]
rs247447	0.81[ASN][1000 genomes]
rs247450	0.90[ASN][1000 genomes]
rs37596	0.93[ASN][1000 genomes]
rs37599	0.93[ASN][1000 genomes]
rs37601	0.96[ASN][1000 genomes]
rs37602	0.93[ASN][1000 genomes]
rs37605	0.94[ASN][1000 genomes]
rs40217	0.87[ASN][1000 genomes]
rs4887827	0.82[ASN][1000 genomes]
rs4887828	0.90[ASN][1000 genomes]
rs8046416	0.88[ASN][1000 genomes]
rs977986	0.94[ASN][1000 genomes]
rs9923834	0.94[ASN][1000 genomes]
rs9928232	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	esv2758432	chr16:75419614-75576971	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	esv2758657	chr16:75419614-75576971	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv457521	chr16:75487758-75603925	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv572979	chr16:75487758-75603925	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS 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	57 gene(s)	inside rSNPs	diseases
10	esv3485939	chr16:75497453-75550284	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	esv3485940	chr16:75497453-75550284	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	nsv572980	chr16:75505046-75549885	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs185053	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75498600-75511800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:75498800-75518600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr16:75499000-75511000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr16:75499000-75511200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr16:75499000-75511200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr16:75499200-75511400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr16:75499200-75511400	Weak transcription	Brain Anterior Caudate	brain
8	chr16:75499200-75519600	Weak transcription	Fetal Intestine Small	intestine
9	chr16:75502400-75518200	Weak transcription	Aorta	Aorta
10	chr16:75505400-75512600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr16:75506000-75512600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr16:75506200-75511600	Weak transcription	Brain Hippocampus Middle	brain
13	chr16:75506200-75517000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr16:75506400-75510800	Weak transcription	Hela-S3	cervix
15	chr16:75506600-75511000	Weak transcription	HMEC	breast
16	chr16:75506800-75510800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr16:75506800-75511400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr16:75506800-75512200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr16:75506800-75512400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr16:75506800-75514200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr16:75506800-75520400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr16:75507000-75512400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr16:75507000-75517600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr16:75507000-75525600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr16:75507200-75511000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr16:75507200-75511000	Weak transcription	Brain Substantia Nigra	brain
27	chr16:75507200-75511200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr16:75507200-75512600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr16:75507400-75512400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr16:75507800-75511200	Weak transcription	Brain Angular Gyrus	brain
31	chr16:75509600-75511400	Weak transcription	Brain Cingulate Gyrus	brain

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