Variant report

Variant	rs9450309
Chromosome Location	chr6:86348743-86348744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86338689..86357756-chr6:86378394..86390434,115	MCF-7	breast:
2	chr6:86326511..86329111-chr6:86347081..86350058,3	K562	blood:
3	chr6:86300873..86305245-chr6:86347697..86356641,19	K562	blood:
4	chr6:86300457..86307827-chr6:86347697..86356337,20	K562	blood:
5	chr6:86317763..86319413-chr6:86348369..86350869,2	K562	blood:
6	chr6:86327554..86329111-chr6:86347081..86350058,2	K562	blood:
7	chr6:86308147..86310058-chr6:86348388..86350658,2	K562	blood:

Variant related genes	Relation type
ENSG00000135317	Chromatin interaction
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12528808	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2229524	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3812137	0.81[ASN][1000 genomes]
rs3812139	0.81[ASN][1000 genomes]
rs4327657	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59744370	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6900270	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6902638	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902904	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6910543	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6913634	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6923017	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930543	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930790	0.87[ASN][1000 genomes]
rs73751215	0.81[ASN][1000 genomes]
rs7744309	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7749600	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752105	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7771187	0.81[ASN][1000 genomes]
rs7771366	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7775788	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344530	0.81[ASN][1000 genomes]
rs9344538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9351063	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9351066	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9353319	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353321	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353323	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9353324	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362223	0.81[ASN][1000 genomes]
rs9362225	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9362226	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444353	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444356	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450286	0.81[ASN][1000 genomes]
rs9450289	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450294	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450295	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450299	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9450300	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450304	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450308	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450313	0.85[EUR][1000 genomes];0.93[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	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9450309	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs9450309	NT5E	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86313400-86349000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr6:86316200-86348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:86316400-86349200	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:86316400-86350600	Strong transcription	Fetal Thymus	thymus
5	chr6:86317000-86349000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:86317400-86349000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:86317600-86349800	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr6:86318600-86348800	Strong transcription	Primary B cells from peripheral blood	blood
9	chr6:86319000-86350000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr6:86319600-86348800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:86319600-86350000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr6:86320200-86350400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr6:86321000-86349600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:86323600-86349000	Strong transcription	Fetal Intestine Large	intestine
15	chr6:86323600-86351200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:86326400-86349200	Strong transcription	Primary hematopoietic stem cells	blood
17	chr6:86328000-86349800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr6:86331400-86349000	Strong transcription	HSMM	muscle
19	chr6:86332400-86349200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:86335200-86349600	Strong transcription	Fetal Muscle Leg	muscle
21	chr6:86335600-86349000	Strong transcription	Adipose Nuclei	Adipose
22	chr6:86335600-86349200	Strong transcription	Fetal Kidney	kidney
23	chr6:86338800-86349000	Strong transcription	Osteobl	bone
24	chr6:86339000-86349200	Strong transcription	NH-A	brain
25	chr6:86339200-86349200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:86340000-86349400	Strong transcription	Primary B cells from cord blood	blood
27	chr6:86340200-86349000	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr6:86340400-86350400	Weak transcription	Aorta	Aorta
29	chr6:86340800-86349000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:86341200-86349400	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr6:86342000-86349000	Strong transcription	HMEC	breast
32	chr6:86342200-86349000	Weak transcription	Fetal Heart	heart
33	chr6:86342400-86348800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:86344400-86349000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:86344800-86348800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:86344800-86348800	Weak transcription	Stomach Mucosa	stomach
37	chr6:86345600-86349200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:86346000-86349400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:86346200-86349800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr6:86346200-86350400	Weak transcription	Fetal Intestine Small	intestine
41	chr6:86346400-86350600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:86346600-86350000	Genic enhancers	HepG2	liver
43	chr6:86346600-86352400	Transcr. at gene 5' and 3'	Dnd41	blood
44	chr6:86347000-86349800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr6:86347000-86349800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:86347000-86350200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:86347000-86350200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr6:86347000-86350200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:86347000-86350400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
50	chr6:86347000-86350400	Genic enhancers	Colon Smooth Muscle	Colon

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