Variant report

Variant	rs9399488
Chromosome Location	chr6:144996435-144996436
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11155365	0.82[EUR][1000 genomes]
rs11155370	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17074004	0.82[EUR][1000 genomes]
rs1980379	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2056745	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6907773	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9373420	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9376837	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9376838	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9386076	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390184	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9390187	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9390188	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9399483	0.82[EUR][1000 genomes]
rs9399486	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9399489	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403578	0.92[AMR][1000 genomes];0.98[EUR][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	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv604822	chr6:144968195-145001887	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1032838	chr6:144978504-145110121	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144981200-145031000	Weak transcription	Placenta	Placenta
2	chr6:144982800-145010000	Weak transcription	Fetal Stomach	stomach
3	chr6:144983000-145024600	Weak transcription	Fetal Kidney	kidney
4	chr6:144985000-145004200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:144986200-145002000	Weak transcription	Small Intestine	intestine
6	chr6:144993000-145000800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:144995000-144999600	Weak transcription	HepG2	liver
8	chr6:144995400-145002000	Weak transcription	Primary T cells from cord blood	blood
9	chr6:144995600-144997000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr6:144995600-144997000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:144995600-144997000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr6:144995600-144998400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr6:144995800-144997000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:144995800-145001800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:144996000-144996600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr6:144996000-144996800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr6:144996000-144997000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr6:144996000-144997000	Flanking Active TSS	Dnd41	blood
19	chr6:144996000-145000000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:144996000-145010000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:144996200-144996600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr6:144996200-144996600	Enhancers	Lung	lung
23	chr6:144996200-144996600	Enhancers	Thymus	Thymus
24	chr6:144996200-144996600	Enhancers	HSMMtube	muscle
25	chr6:144996200-144996800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:144996200-144996800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr6:144996200-144996800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:144996200-144996800	Enhancers	Duodenum Mucosa	Duodenum
29	chr6:144996200-144996800	Enhancers	Fetal Thymus	thymus
30	chr6:144996200-144997000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:144996200-144997000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:144996200-144997000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:144996200-144997000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
34	chr6:144996200-144997000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr6:144996200-144997000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:144996200-144997000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr6:144996200-144997000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:144996200-144997000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:144996200-144997000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr6:144996200-144997000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:144996200-144997000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:144996200-144997000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:144996200-144997000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:144996200-144997000	Enhancers	Esophagus	oesophagus
45	chr6:144996200-144997000	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr6:144996200-144997000	Enhancers	Fetal Muscle Leg	muscle
47	chr6:144996200-144997000	Enhancers	Gastric	stomach
48	chr6:144996200-144997000	Enhancers	Psoas Muscle	Psoas
49	chr6:144996200-144997000	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr6:144996200-144997000	Enhancers	Sigmoid Colon	Sigmoid Colon

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