Variant report

Variant	rs6929755
Chromosome Location	chr6:3986611-3986612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:3985992..3988806-chr6:4017298..4019133,2	MCF-7	breast:
2	chr6:3980920..3982632-chr6:3985928..3988379,2	MCF-7	breast:
3	chr6:3985295..3987675-chr6:3989539..3991361,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272248	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12524454	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525663	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12525919	0.86[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17137399	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959268	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959269	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv1800199	chr6:3986611-4014872	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:3964800-3987400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:3976400-3990800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:3978400-3987200	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:3978600-3986800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:3978600-3991000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:3978600-3991000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:3978800-3987200	Weak transcription	Fetal Stomach	stomach
8	chr6:3978800-3991000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:3978800-3991000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:3978800-3991000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:3979000-3986800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:3979000-3987000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:3979000-3990600	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:3979000-3990800	Weak transcription	HSMM	muscle
15	chr6:3979000-3991000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:3979000-4003200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:3979200-3990600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:3979200-3991000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:3979400-3986800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:3979400-3986800	Weak transcription	Adipose Nuclei	Adipose
21	chr6:3979400-3990800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:3979800-3987200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:3980000-3986800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:3980400-3987600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:3980600-3987600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:3980600-4003600	Weak transcription	Primary B cells from cord blood	blood
27	chr6:3980800-3990800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr6:3981400-3986800	Weak transcription	Pancreas	Pancrea
29	chr6:3982200-3987400	Weak transcription	Fetal Lung	lung
30	chr6:3982400-3990600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:3982600-3986800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:3983000-3987000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:3983000-3987200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:3983000-3991000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:3983400-3987200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:3983400-3987200	Weak transcription	Fetal Kidney	kidney
37	chr6:3983400-3987200	Weak transcription	Psoas Muscle	Psoas
38	chr6:3983800-3990800	Weak transcription	Ovary	ovary
39	chr6:3984600-3986800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:3984800-3986800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:3984800-3987000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr6:3985000-3986800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr6:3985000-3986800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr6:3985000-3986800	Weak transcription	Small Intestine	intestine
45	chr6:3985000-3987200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:3985200-3986800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:3985400-4011000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:3985800-3990800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr6:3986600-3987000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:3986600-3987400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links