Variant report

Variant	rs9393909
Chromosome Location	chr6:28207200-28207201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28205432..28207729-chr6:28233422..28235903,2	K562	blood:
2	chr6:28202355..28207419-chr6:28302691..28306303,4	K562	blood:
3	chr6:28106928..28109553-chr6:28206567..28208256,2	MCF-7	breast:
4	chr6:28206024..28209591-chr6:28211608..28215918,4	MCF-7	breast:
5	chr6:28103041..28105125-chr6:28207182..28210189,3	K562	blood:
6	chr6:28202226..28208942-chr6:28209296..28217649,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269293	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000261839	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11962305	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967137	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1736904	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2299029	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34477097	0.93[AFR][1000 genomes]
rs34787248	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9295768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357067	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9366718	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9368563	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9468317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs967005	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9393909	HLA-A	cis	multi-tissue	Pritchard
rs9393909	BTN3A2	cis	multi-tissue	Pritchard
rs9393909	AL022393.7	cis	Muscle Skeletal	GTEx
rs9393909	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9393909	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28193600-28213400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:28193800-28211800	Weak transcription	Fetal Thymus	thymus
3	chr6:28193800-28218400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:28193800-28218400	Weak transcription	Stomach Mucosa	stomach
5	chr6:28194000-28211000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr6:28194000-28211800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:28194000-28212800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:28194000-28213000	Weak transcription	Thymus	Thymus
9	chr6:28194000-28213600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:28196800-28212400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:28196800-28212400	Weak transcription	Small Intestine	intestine
12	chr6:28196800-28213600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:28197000-28212400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:28198800-28212200	Weak transcription	Hela-S3	cervix
15	chr6:28199200-28213200	Weak transcription	Colonic Mucosa	Colon
16	chr6:28199800-28213600	Weak transcription	NHDF-Ad	bronchial
17	chr6:28200400-28212400	Weak transcription	Fetal Intestine Small	intestine
18	chr6:28200400-28212600	Weak transcription	NHEK	skin
19	chr6:28200800-28212400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:28200800-28212600	Weak transcription	Fetal Heart	heart
21	chr6:28201000-28211000	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:28201000-28211600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:28201000-28212200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:28201000-28212200	Weak transcription	Brain Anterior Caudate	brain
25	chr6:28201000-28212400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:28201000-28212400	Weak transcription	HMEC	breast
27	chr6:28201000-28212800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:28201000-28212800	Weak transcription	Pancreas	Pancrea
29	chr6:28201000-28212800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:28201000-28212800	Weak transcription	Right Ventricle	heart
31	chr6:28201200-28212200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:28201600-28211600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:28201600-28211800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:28201600-28212000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:28201600-28212400	Weak transcription	Esophagus	oesophagus
36	chr6:28201600-28212600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:28201600-28212600	Weak transcription	Brain Angular Gyrus	brain
38	chr6:28201600-28212600	Weak transcription	Fetal Brain Male	brain
39	chr6:28201600-28212800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:28201600-28212800	Weak transcription	Gastric	stomach
41	chr6:28201600-28213000	Weak transcription	HepG2	liver
42	chr6:28201600-28213400	Weak transcription	Fetal Kidney	kidney
43	chr6:28201600-28219400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:28201800-28211000	Weak transcription	Psoas Muscle	Psoas
45	chr6:28201800-28211800	Weak transcription	Osteobl	bone
46	chr6:28201800-28212000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:28202000-28211400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr6:28202000-28211600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:28202000-28211800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:28202000-28212000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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