Variant report

Variant	rs55643343
Chromosome Location	chr9:96057911-96057912
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96057178..96058712-chr9:96213600..96215375,2	MCF-7	breast:
2	chr9:95983716..95985400-chr9:96057478..96060069,2	MCF-7	breast:
3	chr9:96051018..96055450-chr9:96055680..96058903,4	K562	blood:

Variant related genes	Relation type
ENSG00000048828	Chromatin interaction
ENSG00000165238	Chromatin interaction
ENSG00000188938	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10512233	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16909000	0.85[EUR][1000 genomes]
rs16909005	0.90[EUR][1000 genomes]
rs16909016	0.85[EUR][1000 genomes]
rs16936750	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16936752	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1889339	0.93[ASN][1000 genomes]
rs55692827	0.90[EUR][1000 genomes]
rs55706397	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55795421	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56300939	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58895554	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs72743433	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72743435	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72743442	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72743443	0.95[EUR][1000 genomes]
rs72743444	0.85[EUR][1000 genomes]
rs72743445	0.90[EUR][1000 genomes]
rs72743446	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72743449	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	esv3509538	chr9:96056931-96060629	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv3509539	chr9:96056931-96060629	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv3388434	chr9:96057581-96060479	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96027200-96061000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr9:96031400-96062800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:96033000-96067200	Weak transcription	Brain Angular Gyrus	brain
4	chr9:96033400-96062800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:96033400-96067000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:96033400-96077200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:96033600-96060200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:96033600-96061000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:96033600-96072800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:96033800-96060400	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:96047200-96065000	Weak transcription	Fetal Brain Male	brain
12	chr9:96051400-96067800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:96052000-96060800	Weak transcription	Placenta	Placenta
14	chr9:96052200-96066600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:96054400-96058200	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:96055200-96060200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:96055600-96080200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:96056000-96060800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:96056400-96058200	Enhancers	Spleen	Spleen
20	chr9:96056400-96079800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:96056600-96058000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:96056600-96058000	Enhancers	Fetal Thymus	thymus
23	chr9:96056600-96058000	Enhancers	Left Ventricle	heart
24	chr9:96056600-96058000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr9:96056800-96058000	Genic enhancers	Fetal Intestine Small	intestine
26	chr9:96056800-96058000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr9:96056800-96058000	Enhancers	HepG2	liver
28	chr9:96056800-96058200	Enhancers	Primary B cells from peripheral blood	blood
29	chr9:96056800-96059200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:96056800-96067400	Weak transcription	Brain Anterior Caudate	brain
31	chr9:96057000-96058000	Enhancers	Fetal Intestine Large	intestine
32	chr9:96057000-96058000	Enhancers	Right Ventricle	heart
33	chr9:96057000-96058200	Enhancers	Primary B cells from cord blood	blood
34	chr9:96057000-96058200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr9:96057000-96058200	Enhancers	Pancreas	Pancrea
36	chr9:96057000-96059800	Weak transcription	Brain Germinal Matrix	brain
37	chr9:96057200-96058000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr9:96057200-96058000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr9:96057200-96058000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr9:96057200-96058000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr9:96057200-96058000	Bivalent Enhancer	Fetal Stomach	stomach
42	chr9:96057200-96058000	Enhancers	Right Atrium	heart
43	chr9:96057200-96058000	Enhancers	HSMMtube	muscle
44	chr9:96057200-96058400	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr9:96057400-96058000	Enhancers	Duodenum Mucosa	Duodenum
46	chr9:96057400-96059000	Weak transcription	Fetal Heart	heart
47	chr9:96057400-96059800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr9:96057600-96059400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr9:96057600-96059400	Weak transcription	Fetal Brain Female	brain
50	chr9:96057600-96059400	Weak transcription	Gastric	stomach

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