Variant report

Variant	rs3756966
Chromosome Location	chr6:11202604-11202605
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11197881..11200138-chr6:11201320..11203680,2	K562	blood:
2	chr6:11201732..11205267-chr6:11223600..11226865,3	MCF-7	breast:
3	chr6:11201485..11204415-chr6:11205595..11207344,2	MCF-7	breast:

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	0.92[EUR][1000 genomes]
rs10947020	0.83[EUR][1000 genomes]
rs10947021	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10947026	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12190771	0.94[CEU][hapmap]
rs12190858	0.92[EUR][1000 genomes]
rs12205037	0.85[EUR][1000 genomes]
rs12215094	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12215491	0.90[CEU][hapmap]
rs2034	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327332	0.90[CEU][hapmap]
rs3102	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3778169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778170	0.92[EUR][1000 genomes]
rs3778171	0.92[EUR][1000 genomes]
rs3798733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798737	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3798738	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3798740	0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs3798743	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]
rs6912916	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6915811	0.87[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6928520	0.87[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs6937575	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]
rs726230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729747	0.83[CEU][hapmap]
rs9295813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs3756966	NEDD9	cis	Lymphoblastoid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11192800-11202800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:11192800-11207000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:11192800-11207200	Weak transcription	Liver	Liver
4	chr6:11195000-11203200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr6:11195400-11203200	Enhancers	Thymus	Thymus
6	chr6:11195400-11207200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:11195600-11207400	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:11196000-11203000	Weak transcription	Psoas Muscle	Psoas
9	chr6:11197000-11211000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:11197000-11211200	Genic enhancers	HepG2	liver
11	chr6:11197400-11204000	Enhancers	NHDF-Ad	bronchial
12	chr6:11197800-11203200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:11197800-11204600	Strong transcription	Primary B cells from cord blood	blood
14	chr6:11198200-11207000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:11198400-11202800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:11198400-11203000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:11198400-11203000	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:11198400-11203800	Genic enhancers	Osteobl	bone
19	chr6:11198400-11206600	Genic enhancers	A549	lung
20	chr6:11198600-11203600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:11198800-11205000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:11199000-11203000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:11199200-11205400	Weak transcription	Right Ventricle	heart
24	chr6:11199400-11203000	Weak transcription	Fetal Brain Male	brain
25	chr6:11199400-11203200	Weak transcription	Spleen	Spleen
26	chr6:11199400-11212600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:11199600-11204200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:11199600-11204200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:11200200-11203400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:11200200-11204200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:11200200-11204200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:11200200-11204600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
33	chr6:11200400-11202800	Weak transcription	Small Intestine	intestine
34	chr6:11200400-11204600	Genic enhancers	HUVEC	blood vessel
35	chr6:11200400-11205600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr6:11200800-11203200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr6:11200800-11203600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:11200800-11204200	Genic enhancers	NHLF	lung
39	chr6:11201000-11203400	Genic enhancers	HSMMtube	muscle
40	chr6:11201000-11208600	Genic enhancers	Fetal Thymus	thymus
41	chr6:11201200-11202800	Enhancers	Brain Anterior Caudate	brain
42	chr6:11201400-11203000	Enhancers	Brain Hippocampus Middle	brain
43	chr6:11201400-11203200	Enhancers	Primary T cells from cord blood	blood
44	chr6:11201400-11203800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:11201600-11202800	Weak transcription	Adipose Nuclei	Adipose
46	chr6:11201600-11202800	Weak transcription	Fetal Stomach	stomach
47	chr6:11201600-11203000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:11201600-11203000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:11201600-11203000	Weak transcription	Right Atrium	heart
50	chr6:11201600-11203000	Weak transcription	Monocytes-CD14+_RO01746	blood

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