Variant report

Variant	rs10780639
Chromosome Location	chr9:86620546-86620547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86569088..86572971-chr9:86618139..86621506,3	K562	blood:

Variant related genes	Relation type
ENSG00000165118	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10124390	0.85[EUR][1000 genomes]
rs10780640	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10868077	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12004439	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12006540	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12551039	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1572030	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs177042	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs296891	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs296892	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4877814	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4877815	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5018100	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6559753	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6559754	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6559756	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7020841	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7021189	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7045008	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7864367	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7875011	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7875242	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs796000	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs796001	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs796002	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv3328820	chr9:86613612-86634313	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86596400-86632400	Weak transcription	Spleen	Spleen
2	chr9:86596800-86621400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr9:86596800-86621600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:86597000-86621200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr9:86597000-86621600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:86597400-86628800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:86598800-86622400	Weak transcription	Brain Germinal Matrix	brain
8	chr9:86602000-86620800	Weak transcription	NHLF	lung
9	chr9:86602000-86623200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:86602400-86627200	Weak transcription	Left Ventricle	heart
11	chr9:86603800-86621200	Weak transcription	Hela-S3	cervix
12	chr9:86604000-86622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:86604000-86626200	Weak transcription	Pancreas	Pancrea
14	chr9:86604200-86621400	Weak transcription	Thymus	Thymus
15	chr9:86604200-86623400	Weak transcription	Fetal Stomach	stomach
16	chr9:86605000-86622400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:86605200-86620600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:86605400-86622200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:86606000-86624200	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:86607800-86622600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:86607800-86622800	Weak transcription	K562	blood
22	chr9:86611000-86623000	Weak transcription	Psoas Muscle	Psoas
23	chr9:86613200-86621200	Weak transcription	Adipose Nuclei	Adipose
24	chr9:86615600-86621400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:86616800-86620800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:86616800-86621200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr9:86616800-86621400	Weak transcription	HepG2	liver
28	chr9:86616800-86621600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:86616800-86621800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr9:86616800-86623800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:86617000-86621600	Weak transcription	Fetal Lung	lung
32	chr9:86617000-86621600	Weak transcription	Fetal Thymus	thymus
33	chr9:86617000-86622200	Weak transcription	Fetal Brain Female	brain
34	chr9:86617000-86622600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr9:86617000-86622800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr9:86617000-86622800	Weak transcription	Fetal Kidney	kidney
37	chr9:86617400-86621600	Weak transcription	Primary B cells from cord blood	blood
38	chr9:86617600-86620600	Weak transcription	Liver	Liver
39	chr9:86617600-86620800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr9:86617600-86620800	Weak transcription	NHDF-Ad	bronchial
41	chr9:86617600-86621200	Weak transcription	Stomach Mucosa	stomach
42	chr9:86617600-86621200	Weak transcription	HSMM	muscle
43	chr9:86617600-86621600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr9:86617600-86621600	Weak transcription	HUVEC	blood vessel
45	chr9:86617600-86624400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:86617600-86624800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr9:86617600-86625000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr9:86617800-86621200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:86617800-86623600	Weak transcription	A549	lung
50	chr9:86617800-86625800	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links