Variant report

Variant	rs3798743
Chromosome Location	chr6:11212959-11212960
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11211001..11214077-chr6:11215727..11219130,4	K562	blood:
2	chr6:11210641..11214378-chr6:11216495..11219035,4	MCF-7	breast:
3	chr6:11206545..11209352-chr6:11211717..11213636,2	K562	blood:
4	chr6:11211255..11213887-chr6:11228250..11229888,2	MCF-7	breast:
5	chr6:11211756..11214588-chr6:11226503..11228264,2	MCF-7	breast:
6	chr6:11209766..11214077-chr6:11214391..11221251,7	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10807059	0.90[EUR][1000 genomes]
rs10947017	0.89[EUR][1000 genomes]
rs10947020	0.82[EUR][1000 genomes]
rs10947021	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs10947026	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs12190771	0.94[CEU][hapmap]
rs12190858	0.89[EUR][1000 genomes]
rs12205037	0.82[EUR][1000 genomes]
rs12215094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215491	0.95[CEU][hapmap]
rs2034	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2327332	0.90[CEU][hapmap]
rs3102	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs3756966	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3778169	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3778170	0.89[EUR][1000 genomes]
rs3778171	0.89[EUR][1000 genomes]
rs3798733	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798734	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798736	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798737	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs3798738	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs3798740	0.82[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6912916	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915811	0.87[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs6928520	0.87[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6937575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726230	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs729747	0.83[CEU][hapmap]
rs9295813	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3798743	NEDD9	cis	Lymphoblastoid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11201800-11213000	Weak transcription	Esophagus	oesophagus
2	chr6:11203800-11213200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:11203800-11213400	Weak transcription	Brain Germinal Matrix	brain
4	chr6:11204200-11213600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:11204200-11213800	Weak transcription	Brain Substantia Nigra	brain
6	chr6:11204200-11222400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:11205200-11215400	Genic enhancers	NH-A	brain
8	chr6:11205200-11217800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:11206400-11216600	Enhancers	Fetal Muscle Leg	muscle
10	chr6:11206600-11214600	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr6:11206600-11214800	Genic enhancers	Osteobl	bone
12	chr6:11207200-11218600	Strong transcription	Primary B cells from cord blood	blood
13	chr6:11207400-11213800	Enhancers	Fetal Brain Male	brain
14	chr6:11207600-11216800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:11207800-11213000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:11207800-11216000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:11207800-11218200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:11208000-11216200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:11208000-11216400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:11208000-11217200	Strong transcription	GM12878-XiMat	blood
21	chr6:11208200-11218600	Genic enhancers	HUVEC	blood vessel
22	chr6:11208400-11213600	Genic enhancers	Adipose Nuclei	Adipose
23	chr6:11208400-11214600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:11208600-11218200	Strong transcription	Primary B cells from peripheral blood	blood
25	chr6:11208800-11213000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:11208800-11213200	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr6:11208800-11213400	Genic enhancers	NHDF-Ad	bronchial
28	chr6:11209400-11213600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:11209400-11217200	Genic enhancers	Placenta Amnion	Placenta Amnion
30	chr6:11209600-11214000	Genic enhancers	Primary T cells from cord blood	blood
31	chr6:11209600-11214400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr6:11209800-11214200	Genic enhancers	Fetal Thymus	thymus
33	chr6:11209800-11215200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr6:11210000-11218000	Enhancers	Stomach Mucosa	stomach
35	chr6:11210200-11215200	Weak transcription	Small Intestine	intestine
36	chr6:11210200-11215400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr6:11210200-11216800	Genic enhancers	Placenta	Placenta
38	chr6:11210200-11217200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
39	chr6:11210400-11214000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr6:11210400-11214200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr6:11210400-11216200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:11210800-11214600	Strong transcription	Fetal Intestine Large	intestine
43	chr6:11210800-11215000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr6:11211000-11213000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr6:11211000-11213800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
46	chr6:11211000-11214000	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr6:11211000-11214000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr6:11211000-11215400	Strong transcription	Fetal Intestine Small	intestine
49	chr6:11211000-11215400	Genic enhancers	Thymus	Thymus
50	chr6:11211000-11216600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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