Variant report

Variant	rs12463315
Chromosome Location	chr19:18397788-18397789
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:18397731-18398075	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:18397592-18398036	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18396145..18399548-chr19:18528063..18530226,4	K562	blood:
2	chr19:18397375..18399268-chr19:18401136..18404109,3	MCF-7	breast:
3	chr19:18383365..18408325-chr19:18518460..18533256,66	K562	blood:

Variant related genes	Relation type
RPL39P38	TF binding region
ENSG00000221167	Chromatin interaction
ENSG00000130511	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10854164	0.82[EUR][1000 genomes]
rs1421720	0.84[ASN][1000 genomes]
rs17711565	0.81[AMR][1000 genomes]
rs4808777	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60086589	0.82[ASN][1000 genomes]
rs7247767	0.81[ASN][1000 genomes]
rs7248070	0.84[ASN][1000 genomes]
rs8103549	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
5	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
6	nsv911269	chr19:18351674-18418044	Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
7	nsv911270	chr19:18351674-18422364	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
8	nsv911271	chr19:18362940-18453124	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
9	nsv828472	chr19:18377725-18404131	Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
10	esv1833305	chr19:18378219-18408222	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
11	nsv911272	chr19:18378219-18439383	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
12	esv1793726	chr19:18381600-18400786	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	104 gene(s)	inside rSNPs	diseases
13	nsv911273	chr19:18386798-18454825	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	134 gene(s)	inside rSNPs	diseases
14	nsv963018	chr19:18395612-18399311	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12463315	KIAA1683	cis	Thyroid	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18393800-18397800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:18393800-18397800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:18393800-18398000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:18393800-18398000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr19:18393800-18398400	Weak transcription	NH-A	brain
6	chr19:18393800-18399000	Weak transcription	Fetal Kidney	kidney
7	chr19:18393800-18401000	Weak transcription	Thymus	Thymus
8	chr19:18393800-18401200	Weak transcription	Right Atrium	heart
9	chr19:18393800-18402000	Weak transcription	Aorta	Aorta
10	chr19:18394000-18398800	Weak transcription	Fetal Lung	lung
11	chr19:18394000-18398800	Weak transcription	A549	lung
12	chr19:18394000-18400400	Weak transcription	Dnd41	blood
13	chr19:18394000-18400600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr19:18394000-18400800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:18394000-18401200	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:18394000-18401400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:18394000-18401400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr19:18394000-18402000	Weak transcription	Brain Anterior Caudate	brain
19	chr19:18394000-18402800	Weak transcription	Gastric	stomach
20	chr19:18394400-18397800	Weak transcription	Fetal Stomach	stomach
21	chr19:18394400-18399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:18394400-18399000	Weak transcription	Colon Smooth Muscle	Colon
23	chr19:18394400-18399200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr19:18394400-18400400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr19:18394400-18400600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr19:18394400-18400800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:18394400-18401000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:18394400-18402000	Weak transcription	Pancreas	Pancrea
29	chr19:18394400-18402000	Weak transcription	Right Ventricle	heart
30	chr19:18394600-18400600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:18394600-18402200	Weak transcription	Psoas Muscle	Psoas
32	chr19:18395200-18397800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr19:18395400-18398000	Enhancers	Fetal Thymus	thymus
34	chr19:18395400-18399600	Enhancers	Fetal Muscle Leg	muscle
35	chr19:18395600-18397800	Enhancers	Osteobl	bone
36	chr19:18395800-18400600	Weak transcription	Lung	lung
37	chr19:18395800-18400600	Weak transcription	Spleen	Spleen
38	chr19:18396000-18398000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:18396000-18398600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:18396000-18398800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:18396000-18400600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:18396000-18401000	Weak transcription	Colonic Mucosa	Colon
43	chr19:18396000-18402600	Weak transcription	Small Intestine	intestine
44	chr19:18396200-18398200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:18396200-18398800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:18396200-18401000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr19:18396200-18402600	Weak transcription	Liver	Liver
48	chr19:18396400-18398600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:18396400-18398600	Weak transcription	Fetal Intestine Large	intestine
50	chr19:18396400-18398600	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links