Variant report

Variant	rs56300939
Chromosome Location	chr9:96059936-96059937
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95962461..95964580-chr9:96059375..96061154,2	MCF-7	breast:
2	chr9:95988443..95991270-chr9:96059116..96061610,2	MCF-7	breast:
3	chr9:96050206..96051928-chr9:96059478..96062127,2	MCF-7	breast:
4	chr9:95983716..95985400-chr9:96057478..96060069,2	MCF-7	breast:
5	chr9:96050846..96054086-chr9:96058108..96060886,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165238	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];0.93[ASN][1000 genomes]
rs16909000	0.85[EUR][1000 genomes]
rs16909005	0.90[EUR][1000 genomes]
rs16909016	0.85[EUR][1000 genomes]
rs16936750	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16936752	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1889339	0.95[ASN][1000 genomes]
rs55643343	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55692827	0.90[EUR][1000 genomes]
rs55706397	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55795421	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58895554	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs72743433	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72743435	0.90[EUR][1000 genomes];0.96[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	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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:50 , 50 per page) page: 1

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	chr9:96055200-96060200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr9:96055600-96080200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:96056000-96060800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:96056400-96079800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:96056800-96067400	Weak transcription	Brain Anterior Caudate	brain
20	chr9:96057600-96060000	Weak transcription	Colonic Mucosa	Colon
21	chr9:96057600-96060000	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:96057600-96060400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:96057600-96061000	Weak transcription	Stomach Mucosa	stomach
24	chr9:96058000-96060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:96058000-96060600	Weak transcription	Right Ventricle	heart
26	chr9:96058000-96061200	Weak transcription	Left Ventricle	heart
27	chr9:96058000-96062000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr9:96058000-96063200	Weak transcription	Right Atrium	heart
29	chr9:96058200-96060200	Weak transcription	Pancreas	Pancrea
30	chr9:96058200-96061400	Weak transcription	Spleen	Spleen
31	chr9:96058200-96064600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr9:96058200-96064600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr9:96059000-96063800	Enhancers	Fetal Heart	heart
34	chr9:96059200-96060000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:96059400-96060200	Enhancers	HepG2	liver
36	chr9:96059400-96060400	Strong transcription	Fetal Intestine Small	intestine
37	chr9:96059400-96061400	Enhancers	Fetal Thymus	thymus
38	chr9:96059400-96064200	Strong transcription	Fetal Brain Female	brain
39	chr9:96059600-96060200	Strong transcription	Fetal Intestine Large	intestine
40	chr9:96059600-96060400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr9:96059600-96063000	Enhancers	Duodenum Mucosa	Duodenum
42	chr9:96059600-96063000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr9:96059600-96067000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr9:96059800-96060000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr9:96059800-96060000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr9:96059800-96060400	Weak transcription	Gastric	stomach
47	chr9:96059800-96060800	Weak transcription	Psoas Muscle	Psoas
48	chr9:96059800-96061400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr9:96059800-96062000	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr9:96059800-96064600	Strong transcription	Brain Germinal Matrix	brain

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