Variant report

Variant	rs34020099
Chromosome Location	chr9:95961346-95961347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95960782..95962974-chr9:95969485..95971200,2	MCF-7	breast:
2	chr9:95961109..95963310-chr9:96212706..96215085,3	MCF-7	breast:
3	chr9:95961070..95962823-chr9:95969517..95972182,2	K562	blood:
4	chr9:95960515..95962748-chr9:96063970..96065844,2	MCF-7	breast:
5	chr9:95959322..95962228-chr9:95991755..95995134,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10992681	0.87[AMR][1000 genomes]
rs11787888	0.82[AMR][1000 genomes]
rs11790340	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790795	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791377	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791390	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794044	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1936399	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34085543	0.82[AMR][1000 genomes]
rs34739795	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34834050	0.82[AMR][1000 genomes]
rs35305079	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35438843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35712744	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36101213	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61275172	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019910	0.83[AMR][1000 genomes]
rs7031721	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7043649	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7046965	0.83[AMR][1000 genomes]
rs72743404	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv824983	chr9:95902154-95978408	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	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
6	nsv614880	chr9:95930572-95978265	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv415527	chr9:95960867-95961471	Weak transcription Enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95950800-95967400	Enhancers	Fetal Heart	heart
2	chr9:95954600-95961600	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr9:95955600-95961600	Enhancers	Rectal Mucosa Donor 29	rectum
4	chr9:95955800-95985600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:95956600-95962600	Weak transcription	Brain Angular Gyrus	brain
6	chr9:95956800-95965000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:95957000-95963800	Weak transcription	Fetal Kidney	kidney
8	chr9:95957000-95973400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:95957200-95963200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:95957200-95963400	Weak transcription	Stomach Mucosa	stomach
11	chr9:95957400-95962200	Weak transcription	Fetal Brain Male	brain
12	chr9:95957400-95962200	Weak transcription	Fetal Brain Female	brain
13	chr9:95957400-95963200	Weak transcription	Fetal Lung	lung
14	chr9:95958000-95963400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr9:95958200-95963400	Weak transcription	Esophagus	oesophagus
16	chr9:95958200-95966200	Enhancers	Placenta	Placenta
17	chr9:95958200-95972800	Enhancers	Left Ventricle	heart
18	chr9:95958200-95975600	Enhancers	Pancreas	Pancrea
19	chr9:95958600-95962800	Enhancers	Stomach Smooth Muscle	stomach
20	chr9:95959000-95961600	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr9:95959000-95961800	Enhancers	HepG2	liver
22	chr9:95959000-95967200	Weak transcription	Small Intestine	intestine
23	chr9:95959200-95962400	Weak transcription	Brain Anterior Caudate	brain
24	chr9:95959200-95970200	Weak transcription	Lung	lung
25	chr9:95959400-95963600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr9:95959600-95962800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr9:95960000-95961400	Enhancers	Brain Cingulate Gyrus	brain
28	chr9:95960000-95961400	Enhancers	Fetal Intestine Large	intestine
29	chr9:95960000-95961600	Enhancers	A549	lung
30	chr9:95960000-95962400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:95960200-95961600	Enhancers	Right Atrium	heart
32	chr9:95960200-95964800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:95960400-95961400	Enhancers	Psoas Muscle	Psoas
34	chr9:95960400-95961600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr9:95960400-95971400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr9:95960600-95962800	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:95960600-95975800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:95960800-95962800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr9:95960800-95963600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:95961000-95961600	Enhancers	Duodenum Mucosa	Duodenum
41	chr9:95961000-95961600	Enhancers	Gastric	stomach
42	chr9:95961000-95962200	Weak transcription	Right Ventricle	heart
43	chr9:95961000-95962800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr9:95961000-95962800	Weak transcription	Fetal Muscle Leg	muscle
45	chr9:95961000-95963000	Strong transcription	Fetal Intestine Small	intestine
46	chr9:95961000-95963200	Weak transcription	Fetal Thymus	thymus
47	chr9:95961000-95963400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:95961200-95961400	Enhancers	Colonic Mucosa	Colon
49	chr9:95961200-95961400	Enhancers	Spleen	Spleen
50	chr9:95961200-95962800	Weak transcription	Brain Germinal Matrix	brain

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