Variant report

Variant	rs9399479
Chromosome Location	chr6:144879815-144879816
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	chr6:144863103..144865561-chr6:144876980..144880053,3	K562	blood:
2	chr6:144878863..144881142-chr6:144883798..144886467,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10499231	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1358433	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091485	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2876586	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3793134	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3793135	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812245	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812246	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4499947	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4896729	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6570637	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6915747	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7749805	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7749957	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7754789	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7767389	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7770106	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7770800	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9376822	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9390171	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390173	0.91[EUR][1000 genomes]
rs9399478	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9496995	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9497006	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951571	0.87[EUR][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	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1015228	chr6:144780458-144989321	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv538462	chr6:144780458-144989321	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144807400-144904000	Weak transcription	Brain Substantia Nigra	brain
2	chr6:144812400-144881000	Weak transcription	Stomach Mucosa	stomach
3	chr6:144815200-144881000	Weak transcription	NHEK	skin
4	chr6:144816600-144881400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:144837200-144880800	Weak transcription	Brain Angular Gyrus	brain
6	chr6:144850400-144903200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:144850400-144903200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:144850400-144904200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:144850600-144881600	Weak transcription	Brain Anterior Caudate	brain
10	chr6:144853600-144896400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:144854600-144881200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:144857200-144904000	Weak transcription	Psoas Muscle	Psoas
13	chr6:144858200-144887800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr6:144861200-144885000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:144864800-144885200	Weak transcription	Colonic Mucosa	Colon
16	chr6:144864800-144885800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr6:144864800-144899000	Weak transcription	Small Intestine	intestine
18	chr6:144866200-144881600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:144867400-144903800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:144869600-144887000	Strong transcription	Primary hematopoietic stem cells	blood
21	chr6:144869800-144885600	Strong transcription	Adipose Nuclei	Adipose
22	chr6:144870000-144880200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:144870800-144898400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:144871200-144880800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr6:144871400-144880200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:144872000-144881600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:144872000-144903000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr6:144873000-144903200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:144873000-144903800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:144873200-144881000	Weak transcription	NH-A	brain
31	chr6:144874000-144880000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:144874000-144904200	Weak transcription	Placenta	Placenta
33	chr6:144874400-144881400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:144875200-144881000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr6:144875800-144880400	Strong transcription	HSMM	muscle
36	chr6:144876400-144880000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:144876600-144881000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:144876800-144881200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr6:144877000-144895600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:144877000-144898000	Weak transcription	Right Ventricle	heart
41	chr6:144877000-144898200	Weak transcription	Fetal Intestine Small	intestine
42	chr6:144877000-144903000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:144877000-144904200	Weak transcription	Fetal Stomach	stomach
44	chr6:144877200-144880800	Weak transcription	Osteobl	bone
45	chr6:144878000-144881400	Weak transcription	Aorta	Aorta
46	chr6:144878000-144903400	Weak transcription	Fetal Brain Male	brain
47	chr6:144878400-144880800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:144878400-144880800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:144878400-144881200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:144878400-144881200	Weak transcription	HMEC	breast

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