Variant report

Variant	rs2038136
Chromosome Location	chr6:24645947-24645948
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24644992..24647314-chr6:24719656..24721157,2	MCF-7	breast:
2	chr6:24645396..24648521-chr6:24658092..24661192,3	K562	blood:
3	chr6:24645218..24647641-chr6:24665331..24668427,5	MCF-7	breast:
4	chr6:24645863..24648986-chr6:24665821..24668897,5	MCF-7	breast:
5	chr6:24645396..24648552-chr6:24658188..24661192,4	K562	blood:
6	chr6:24645670..24648708-chr6:24654981..24659486,5	MCF-7	breast:
7	chr1:162530645..162531244-chr6:24645762..24646411,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000112304	Chromatin interaction
ENSG00000111802	Chromatin interaction
ENSG00000259788	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1047782	0.81[ASN][1000 genomes]
rs1555089	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555090	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883592	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883594	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038135	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038137	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2038138	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038139	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143341	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2143342	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2179515	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2206525	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2223590	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235677	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328846	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712835	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456622	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456624	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6903205	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903738	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906247	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917660	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6923143	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923652	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923845	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923867	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935753	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938069	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6938411	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs761100	0.93[ASN][1000 genomes]
rs761101	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741572	0.97[ASN][1000 genomes]
rs7751357	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7755563	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7755579	0.81[EUR][1000 genomes]
rs7755983	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7759417	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7759592	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7759747	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760198	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356940	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9356941	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358777	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358778	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358780	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9358783	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358784	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366573	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9366574	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9366575	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366576	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379676	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379678	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9393570	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393571	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461044	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467244	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467245	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467249	0.83[AMR][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	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv601164	chr6:24625091-24661599	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv601165	chr6:24632642-24666007	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2038136	KIAA0319	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24643600-24647000	Active TSS	Fetal Brain Female	brain
2	chr6:24644000-24646800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr6:24644000-24647000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:24644200-24647000	Active TSS	Brain Anterior Caudate	brain
5	chr6:24645400-24646000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:24645400-24646000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
7	chr6:24645400-24646000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr6:24645400-24647000	Active TSS	Brain Angular Gyrus	brain
9	chr6:24645600-24646000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:24645600-24646000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:24645600-24646000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:24645600-24646000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:24645600-24646000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
14	chr6:24645600-24646000	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr6:24645600-24646000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:24645600-24646000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:24645600-24646000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:24645600-24646000	Bivalent Enhancer	Fetal Heart	heart
19	chr6:24645600-24646000	Flanking Bivalent TSS/Enh	HepG2	liver
20	chr6:24645600-24646200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:24645600-24646200	Flanking Bivalent TSS/Enh	Dnd41	blood
22	chr6:24645600-24646400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:24645600-24646600	Active TSS	Colon Smooth Muscle	Colon
24	chr6:24645600-24646600	Active TSS	A549	lung
25	chr6:24645600-24646600	Active TSS	Hela-S3	cervix
26	chr6:24645600-24646800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:24645600-24646800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr6:24645600-24646800	Active TSS	Brain Germinal Matrix	brain
29	chr6:24645600-24646800	Active TSS	Brain Substantia Nigra	brain
30	chr6:24645600-24647000	Active TSS	H1 Cell Line	embryonic stem cell
31	chr6:24645600-24647000	Active TSS	H9 Cell Line	embryonic stem cell
32	chr6:24645600-24647000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr6:24645600-24647000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:24645600-24647000	Active TSS	Brain Cingulate Gyrus	brain
35	chr6:24645600-24647000	Active TSS	Brain Hippocampus Middle	brain
36	chr6:24645600-24647000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:24645600-24647000	Flanking Active TSS	GM12878-XiMat	blood
38	chr6:24645600-24647000	Flanking Active TSS	NHEK	skin
39	chr6:24645800-24646000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:24645800-24646000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:24645800-24646000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:24645800-24646000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:24645800-24646000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:24645800-24646000	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr6:24645800-24646000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:24645800-24646000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr6:24645800-24646000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr6:24645800-24646000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
49	chr6:24645800-24646000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:24645800-24646000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links