Variant report

Variant	rs72743446
Chromosome Location	chr9:96077992-96077993
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	chr9:96072987..96083429-chr9:96209751..96218385,15	MCF-7	breast:
2	chr9:96077920..96081969-chr9:96088164..96091770,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM120A-4	chr9:96077770-96079913	NONHSAT133246

Variant related genes	Relation type
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10512233	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16909000	0.83[EUR][1000 genomes]
rs16909005	0.89[EUR][1000 genomes]
rs16909016	0.94[EUR][1000 genomes]
rs16936750	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16936752	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1889339	0.86[ASN][1000 genomes]
rs55643343	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55692827	0.89[EUR][1000 genomes]
rs55706397	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55795421	0.95[EUR][1000 genomes]
rs56300939	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58895554	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59491442	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72743433	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72743435	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72743442	0.84[EUR][1000 genomes]
rs72743443	0.84[EUR][1000 genomes]
rs72743444	0.94[EUR][1000 genomes]
rs72743445	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743448	0.89[EUR][1000 genomes]
rs72743449	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72743451	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96055600-96080200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr9:96056400-96079800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr9:96061600-96079000	Weak transcription	Gastric	stomach
4	chr9:96063800-96088600	Weak transcription	Right Atrium	heart
5	chr9:96065000-96079200	Weak transcription	Colonic Mucosa	Colon
6	chr9:96065200-96080000	Weak transcription	Spleen	Spleen
7	chr9:96066000-96082800	Weak transcription	Fetal Thymus	thymus
8	chr9:96067200-96081200	Weak transcription	Fetal Heart	heart
9	chr9:96067600-96079200	Weak transcription	Right Ventricle	heart
10	chr9:96067600-96086800	Weak transcription	Fetal Brain Male	brain
11	chr9:96067800-96086800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:96068200-96086200	Weak transcription	Brain Anterior Caudate	brain
13	chr9:96068400-96082400	Weak transcription	Brain Angular Gyrus	brain
14	chr9:96068400-96100400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr9:96068600-96079200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:96068600-96080200	Weak transcription	Left Ventricle	heart
17	chr9:96068800-96080800	Weak transcription	Psoas Muscle	Psoas
18	chr9:96068800-96082600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr9:96069200-96079400	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:96069400-96079600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr9:96069400-96080000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:96070600-96087800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:96071400-96078800	Weak transcription	Brain Germinal Matrix	brain
24	chr9:96071400-96079000	Weak transcription	Fetal Stomach	stomach
25	chr9:96072600-96079000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:96074000-96088600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:96075200-96079200	Weak transcription	Pancreas	Pancrea
28	chr9:96075200-96081000	Weak transcription	Placenta	Placenta
29	chr9:96075400-96078200	Weak transcription	Stomach Mucosa	stomach
30	chr9:96075400-96078400	Weak transcription	Fetal Lung	lung
31	chr9:96075400-96079000	Weak transcription	Fetal Intestine Large	intestine
32	chr9:96075400-96079400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr9:96075400-96080400	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:96075600-96078800	Enhancers	HepG2	liver
35	chr9:96076200-96088400	Weak transcription	A549	lung
36	chr9:96077000-96083800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr9:96077000-96085200	Strong transcription	Fetal Brain Female	brain
38	chr9:96077200-96081400	Strong transcription	Stomach Smooth Muscle	stomach
39	chr9:96077600-96078000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
40	chr9:96077600-96078800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr9:96077800-96079000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr9:96077800-96079000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr9:96077800-96079000	Weak transcription	Fetal Intestine Small	intestine

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