Variant report

Variant	rs55784543
Chromosome Location	chr6:38669410-38669411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38656830..38658689-chr6:38669303..38670813,2	MCF-7	breast:
2	chr6:38606456..38608908-chr6:38667468..38670067,2	MCF-7	breast:
3	chr6:38654394..38655965-chr6:38667989..38670845,2	MCF-7	breast:
4	chr6:38668625..38670754-chr9:86321990..86324896,2	K562	blood:
5	chr6:38626742..38628981-chr6:38666689..38669446,2	K562	blood:

Variant related genes	Relation type
ENSG00000183826	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10447398	0.82[ASN][1000 genomes]
rs10484854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191152	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198212	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214452	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72856516	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38641200-38670000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:38642800-38669800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:38646000-38670000	Weak transcription	A549	lung
4	chr6:38648800-38669800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:38651200-38669800	Weak transcription	HSMM	muscle
6	chr6:38651200-38670000	Weak transcription	Fetal Kidney	kidney
7	chr6:38653000-38670000	Weak transcription	NHDF-Ad	bronchial
8	chr6:38654400-38669800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:38655200-38669800	Weak transcription	Pancreas	Pancrea
10	chr6:38655200-38670000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:38657000-38669800	Weak transcription	Colonic Mucosa	Colon
12	chr6:38657000-38669800	Weak transcription	Lung	lung
13	chr6:38657000-38670000	Weak transcription	Left Ventricle	heart
14	chr6:38657000-38670000	Weak transcription	Psoas Muscle	Psoas
15	chr6:38657600-38669600	Weak transcription	Fetal Brain Male	brain
16	chr6:38663600-38670200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:38665200-38669800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
18	chr6:38665200-38670000	Weak transcription	Right Atrium	heart
19	chr6:38665600-38669600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr6:38666600-38669600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:38666600-38669800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:38666600-38670000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:38666800-38670000	Weak transcription	Brain Angular Gyrus	brain
24	chr6:38667000-38670000	Weak transcription	Small Intestine	intestine
25	chr6:38667400-38670000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:38667800-38669600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:38668000-38669600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
28	chr6:38668000-38669600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
29	chr6:38668000-38669600	ZNF genes & repeats	GM12878-XiMat	blood
30	chr6:38668000-38669600	ZNF genes & repeats	K562	blood
31	chr6:38668000-38669800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:38668200-38669800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr6:38668400-38669600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:38668400-38669800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:38668400-38669800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:38668400-38669800	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:38668400-38669800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:38668400-38670000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:38668400-38670000	Weak transcription	Adipose Nuclei	Adipose
40	chr6:38668400-38670000	Enhancers	Liver	Liver
41	chr6:38668400-38670000	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:38668400-38670000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:38668400-38670000	Weak transcription	Fetal Thymus	thymus
44	chr6:38668400-38670000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:38668400-38670000	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr6:38668400-38670200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:38668600-38669800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:38668600-38669800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr6:38668600-38670000	Weak transcription	Fetal Lung	lung
50	chr6:38669000-38669800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links