Variant report

Variant	rs55779730
Chromosome Location	chr6:163820612-163820613
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	chr6:163820034..163822360-chr6:163835389..163837208,2	MCF-7	breast:
2	chr6:163820462..163822214-chr6:163823879..163825565,2	K562	blood:

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11962088	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11964436	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1414724	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1591536	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16894934	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16895015	0.82[ASN][1000 genomes]
rs1737319	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1737320	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1737324	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1737325	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1737326	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1764010	0.82[ASN][1000 genomes]
rs1764011	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1764012	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1764013	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1764015	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1764019	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2064230	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2064231	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2065857	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34979127	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3763197	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3857503	0.89[ASN][1000 genomes]
rs3857504	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3904720	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4263561	0.89[ASN][1000 genomes]
rs56062115	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6921172	0.85[ASN][1000 genomes]
rs6939218	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs718878	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs718879	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73013582	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73013591	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73015309	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73015318	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73015387	0.83[ASN][1000 genomes]
rs7758706	0.86[ASN][1000 genomes]
rs7772756	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9364687	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1791729	chr6:163814557-163836689	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55779730	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163809800-163825600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:163818000-163822200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:163818000-163822200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:163818000-163822600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:163818000-163826800	Weak transcription	Gastric	stomach
6	chr6:163818200-163821000	Weak transcription	Esophagus	oesophagus
7	chr6:163818200-163822000	Enhancers	Adipose Nuclei	Adipose
8	chr6:163818200-163825600	Weak transcription	Lung	lung
9	chr6:163818200-163826200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:163818200-163826800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:163818400-163825200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:163818400-163825400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:163818400-163825400	Weak transcription	Right Atrium	heart
14	chr6:163818600-163821000	Enhancers	Brain Substantia Nigra	brain
15	chr6:163818600-163821400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:163818600-163822000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:163818600-163823400	Weak transcription	Fetal Heart	heart
18	chr6:163818800-163821600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:163818800-163822000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:163818800-163825800	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:163818800-163826400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:163819000-163820800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr6:163819000-163824000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:163819400-163821800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr6:163819400-163822600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:163819600-163822400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:163819800-163825000	Enhancers	Placenta	Placenta
28	chr6:163820000-163821200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:163820000-163825600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:163820200-163821200	Enhancers	Brain Hippocampus Middle	brain
31	chr6:163820200-163821400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:163820200-163823000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:163820200-163823000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:163820200-163823200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:163820200-163825600	Weak transcription	Spleen	Spleen
36	chr6:163820200-163825800	Weak transcription	Psoas Muscle	Psoas
37	chr6:163820200-163826000	Weak transcription	Brain Germinal Matrix	brain
38	chr6:163820200-163826000	Weak transcription	Fetal Brain Female	brain
39	chr6:163820200-163826800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:163820400-163822400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:163820400-163822600	Weak transcription	Brain Anterior Caudate	brain
42	chr6:163820400-163822600	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr6:163820400-163823000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr6:163820400-163824600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:163820400-163824600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:163820400-163824800	Weak transcription	Brain Angular Gyrus	brain
47	chr6:163820400-163825600	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:163820400-163826000	Weak transcription	Ovary	ovary
49	chr6:163820400-163826800	Weak transcription	GM12878-XiMat	blood
50	chr6:163820600-163825400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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