Variant report

Variant	rs66990486
Chromosome Location	chr9:100680919-100680920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100679350..100681181-chr9:100715024..100716909,2	K562	blood:
2	chr9:100679777..100682034-chr9:100778305..100780071,2	K562	blood:
3	chr9:100678422..100708679-chr9:100734559..100755577,174	K562	blood:
4	chr9:100634662..100636711-chr9:100679210..100681058,2	K562	blood:
5	chr9:100679521..100682199-chr9:101551039..101553640,2	K562	blood:
6	chr9:100679913..100686278-chr9:100816188..100820459,11	K562	blood:
7	chr9:100675954..100709047-chr9:100737887..100755543,175	K562	blood:
8	chr9:100661983..100664921-chr9:100679667..100682904,3	MCF-7	breast:
9	chr9:100680787..100683644-chr9:100817248..100819899,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000236896	Chromatin interaction
ENSG00000095380	Chromatin interaction
ENSG00000165138	Chromatin interaction
ENSG00000136938	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10760021	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10760022	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10984297	0.93[ASN][1000 genomes]
rs10984349	0.97[ASN][1000 genomes]
rs10984361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984373	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10984375	0.83[ASN][1000 genomes]
rs10984405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10984462	0.82[ASN][1000 genomes]
rs10984466	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10984499	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10984506	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1127703	0.97[ASN][1000 genomes]
rs12235434	0.97[ASN][1000 genomes]
rs12236440	0.97[ASN][1000 genomes]
rs12237296	0.97[ASN][1000 genomes]
rs12377604	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1475695	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1475696	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17431614	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17431934	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2417577	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3183927	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3183928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3758253	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3758254	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3780416	0.97[ASN][1000 genomes]
rs3780417	0.97[ASN][1000 genomes]
rs3780418	0.97[ASN][1000 genomes]
rs3780419	0.97[ASN][1000 genomes]
rs3780420	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3808894	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3824496	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4631576	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4743145	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743147	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55737216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67975003	0.82[ASN][1000 genomes]
rs7030887	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030907	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753548	0.89[ASN][1000 genomes]
rs72753572	0.82[ASN][1000 genomes]
rs755109	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7861658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv525113	chr9:100669799-100686815	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv524282	chr9:100677166-100684757	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100658800-100681800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:100662800-100684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:100667200-100684200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:100670000-100684200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:100670800-100684200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:100672800-100684200	Weak transcription	Esophagus	oesophagus
7	chr9:100673000-100684000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:100673200-100682200	Weak transcription	Stomach Mucosa	stomach
9	chr9:100673400-100681000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:100673600-100684000	Weak transcription	NHDF-Ad	bronchial
11	chr9:100673800-100683400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:100673800-100683400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:100673800-100684000	Weak transcription	Aorta	Aorta
14	chr9:100673800-100684200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr9:100673800-100684400	Weak transcription	Spleen	Spleen
16	chr9:100674600-100682800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:100674600-100684000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:100675200-100683800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:100675200-100684000	Weak transcription	Colonic Mucosa	Colon
20	chr9:100675200-100684000	Weak transcription	A549	lung
21	chr9:100675200-100684000	Weak transcription	NH-A	brain
22	chr9:100675200-100684200	Weak transcription	Ovary	ovary
23	chr9:100675400-100681000	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:100675400-100682000	Weak transcription	Brain Substantia Nigra	brain
25	chr9:100675400-100684000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr9:100675400-100684000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:100675400-100684000	Weak transcription	Fetal Heart	heart
28	chr9:100675400-100684000	Weak transcription	Psoas Muscle	Psoas
29	chr9:100675400-100684000	Weak transcription	HUVEC	blood vessel
30	chr9:100675400-100684000	Weak transcription	Osteobl	bone
31	chr9:100675600-100684000	Weak transcription	NHLF	lung
32	chr9:100675800-100681600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:100675800-100683000	Weak transcription	Fetal Intestine Small	intestine
34	chr9:100676000-100681400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:100676000-100682800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr9:100676000-100684000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr9:100676200-100683800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:100676200-100684000	Weak transcription	Fetal Brain Male	brain
39	chr9:100676200-100684200	Weak transcription	Gastric	stomach
40	chr9:100676400-100684000	Weak transcription	Brain Angular Gyrus	brain
41	chr9:100676600-100681000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:100677000-100682400	Weak transcription	GM12878-XiMat	blood
43	chr9:100677400-100684000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:100677600-100683400	Weak transcription	HMEC	breast
45	chr9:100677800-100682200	Weak transcription	Hela-S3	cervix
46	chr9:100678200-100683200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr9:100678200-100683200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:100678200-100684000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:100678400-100681600	Weak transcription	Brain Germinal Matrix	brain
50	chr9:100678400-100682000	Weak transcription	Primary B cells from cord blood	blood

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