Variant report

Variant	rs12972490
Chromosome Location	chr19:36524291-36524292
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	chr19:36523422-36524305	U87	brain:	n/a	n/a
2	REST	chr19:36522810-36524431	H1-neurons	neurons:	n/a	chr19:36523635-36523642 chr19:36523011-36523029 chr19:36523488-36523501 chr19:36523770-36523783
3	POLR2A	chr19:36523709-36524350	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAZ	chr19:36522691-36524331	IMR90	lung:	n/a	chr19:36523773-36523783 chr19:36524013-36524022
5	POLR2A	chr19:36523555-36524302	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36512890..36520143-chr19:36521963..36527491,9	K562	blood:
2	chr19:36524290..36526311-chr19:36531159..36533214,2	MCF-7	breast:

Variant related genes	Relation type
CLIP3	TF binding region
ENSG00000105270	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10407011	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10414679	0.80[ASN][1000 genomes]
rs10414877	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10420353	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10421966	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10423651	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10425692	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10426582	0.98[ASN][1000 genomes]
rs12462432	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12462632	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12462674	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12976505	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12976812	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12977814	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12978482	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12979093	0.98[ASN][1000 genomes]
rs12981654	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17639286	0.96[EUR][1000 genomes]
rs2023865	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2239510	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34906485	0.90[ASN][1000 genomes]
rs35125548	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35875194	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3826995	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4461192	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4805154	0.90[ASN][1000 genomes]
rs4805155	0.98[ASN][1000 genomes]
rs4806252	0.97[ASN][1000 genomes]
rs4806253	0.99[ASN][1000 genomes]
rs71337524	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs721542	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7250448	0.96[ASN][1000 genomes]
rs7259592	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7260609	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8103569	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv911641	chr19:36473677-36536938	Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers 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 target site	26 gene(s)	inside rSNPs	diseases
6	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36506400-36544400	Weak transcription	GM12878-XiMat	blood
2	chr19:36506800-36532400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:36507000-36532200	Weak transcription	Hela-S3	cervix
4	chr19:36508800-36532400	Weak transcription	NHEK	skin
5	chr19:36513600-36525600	Weak transcription	K562	blood
6	chr19:36515200-36527600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr19:36515400-36544600	Weak transcription	Pancreas	Pancrea
8	chr19:36516400-36532400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:36517000-36526400	Weak transcription	HepG2	liver
10	chr19:36518800-36532200	Weak transcription	A549	lung
11	chr19:36522200-36524400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:36522200-36524400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:36522800-36524400	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr19:36522800-36524400	Active TSS	Rectal Smooth Muscle	rectum
15	chr19:36523000-36524400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr19:36523000-36524400	Active TSS	Colon Smooth Muscle	Colon
17	chr19:36523000-36524400	Weak transcription	Dnd41	blood
18	chr19:36523000-36524600	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr19:36523200-36524400	Enhancers	Primary B cells from peripheral blood	blood
20	chr19:36523200-36524400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:36523200-36524400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:36523200-36524400	Active TSS	Brain Hippocampus Middle	brain
23	chr19:36523200-36524400	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr19:36523800-36524400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr19:36523800-36524400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr19:36523800-36524400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:36523800-36524400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:36523800-36524400	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr19:36523800-36525800	Weak transcription	Gastric	stomach
30	chr19:36524000-36524400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:36524000-36524400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:36524000-36524400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr19:36524000-36524400	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr19:36524000-36524400	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr19:36524000-36524400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr19:36524000-36524400	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr19:36524000-36524400	Flanking Active TSS	Fetal Brain Male	brain
38	chr19:36524000-36524400	Flanking Active TSS	Fetal Brain Female	brain
39	chr19:36524000-36524400	Flanking Active TSS	Fetal Kidney	kidney
40	chr19:36524000-36524400	Flanking Active TSS	Fetal Lung	lung
41	chr19:36524000-36524400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
42	chr19:36524000-36524400	Flanking Active TSS	Osteobl	bone
43	chr19:36524000-36525400	Weak transcription	Lung	lung
44	chr19:36524000-36525600	Weak transcription	Liver	Liver
45	chr19:36524000-36525600	Weak transcription	Spleen	Spleen
46	chr19:36524000-36526000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr19:36524000-36526000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:36524000-36526000	Weak transcription	Esophagus	oesophagus
49	chr19:36524000-36529400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr19:36524000-36532000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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