Variant report

Variant	rs12258688
Chromosome Location	chr10:18950787-18950788
allele	C/T
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	IRF1	chr10:18950275-18951108	K562	blood:	n/a	chr10:18950399-18950408 chr10:18950981-18950994
2	POLR2A	chr10:18950575-18951332	A549	lung:	n/a	n/a
3	POLR2A	chr10:18950074-18951237	K562	blood:	n/a	n/a
4	CHD1	chr10:18946884-18951792	IMR90	lung:	n/a	chr10:18948546-18948556 chr10:18948735-18948745
5	POLR2A	chr10:18949923-18951350	HepG2	liver:	n/a	n/a
6	POLR2A	chr10:18950606-18950787	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAFK	chr10:18950540-18950942	HepG2	liver:	n/a	n/a
8	JUND	chr10:18950666-18951003	K562	blood:	n/a	n/a
9	POLR2A	chr10:18946803-18951639	IMR90	lung:	n/a	n/a
10	POLR2A	chr10:18950486-18951025	GM12878	blood:	n/a	n/a
11	POLR2A	chr10:18950108-18951270	GM12878	blood:	n/a	n/a
12	POLR2A	chr10:18950080-18951470	HepG2	liver:	n/a	n/a
13	POLR2A	chr10:18950705-18950913	MCF10A-Er-Src	breast:	n/a	n/a
14	WRNIP1	chr10:18950714-18951210	GM12878	blood:	n/a	n/a
15	POLR2A	chr10:18950601-18950960	K562	blood:	n/a	n/a
16	TBL1XR1	chr10:18950472-18950989	K562	blood:	n/a	n/a
17	POLR2A	chr10:18950523-18951059	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18909074..18910706-chr10:18949247..18951149,2	K562	blood:
2	chr10:18937279..18942257-chr10:18944156..18951752,16	MCF-7	breast:

Variant related genes	Relation type
ARL5B-AS1	TF binding region
ENSG00000241058	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10466095	0.93[AFR][1000 genomes]
rs10508564	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11014986	0.80[AFR][1000 genomes]
rs11014994	0.89[AFR][1000 genomes]
rs11015019	0.92[AFR][1000 genomes]
rs11015036	0.92[AFR][1000 genomes]
rs11015184	0.92[AFR][1000 genomes]
rs11015254	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11015323	0.83[AMR][1000 genomes]
rs11015443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11498244	0.81[AFR][1000 genomes]
rs12246317	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12246433	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12247548	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12247869	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12250601	0.93[AFR][1000 genomes]
rs12255014	0.87[AFR][1000 genomes]
rs12258306	0.93[AFR][1000 genomes]
rs12267659	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12269605	0.97[AFR][1000 genomes]
rs16917589	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs16917615	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs16917628	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17363677	0.92[AFR][1000 genomes]
rs28794621	1.00[AMR][1000 genomes]
rs4614337	0.97[AFR][1000 genomes]
rs59666381	0.80[AFR][1000 genomes]
rs7088674	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7100918	0.90[AFR][1000 genomes];0.83[AMR][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	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18947000-18951200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr10:18947400-18951600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:18948800-18951200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr10:18949000-18954000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:18949400-18950800	Active TSS	HepG2	liver
6	chr10:18949400-18951000	Enhancers	Primary B cells from peripheral blood	blood
7	chr10:18949400-18951200	Enhancers	Brain Substantia Nigra	brain
8	chr10:18949400-18951400	Flanking Active TSS	Dnd41	blood
9	chr10:18949400-18973200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr10:18949600-18950800	Enhancers	Ovary	ovary
11	chr10:18949600-18951000	Enhancers	Primary B cells from cord blood	blood
12	chr10:18949600-18951000	Enhancers	Aorta	Aorta
13	chr10:18949600-18951000	Enhancers	Brain Anterior Caudate	brain
14	chr10:18949600-18951000	Enhancers	Esophagus	oesophagus
15	chr10:18949600-18951000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr10:18949600-18951200	Enhancers	Gastric	stomach
17	chr10:18949600-18951200	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr10:18949600-18951400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr10:18949600-18951400	Enhancers	Brain Hippocampus Middle	brain
20	chr10:18949600-18951400	Enhancers	Colon Smooth Muscle	Colon
21	chr10:18949600-18951400	Enhancers	Fetal Brain Male	brain
22	chr10:18949600-18951600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr10:18949600-18951800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:18949600-18952400	Enhancers	Primary T cells fromperipheralblood	blood
25	chr10:18949600-18952400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:18949600-18953800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr10:18949600-18957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr10:18949600-18972000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr10:18949800-18950800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr10:18949800-18950800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr10:18949800-18950800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr10:18949800-18950800	Enhancers	Fetal Kidney	kidney
33	chr10:18949800-18950800	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr10:18949800-18951000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr10:18949800-18951000	Flanking Active TSS	Liver	Liver
36	chr10:18949800-18951000	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr10:18949800-18951000	Enhancers	Stomach Mucosa	stomach
38	chr10:18949800-18951000	Enhancers	Spleen	Spleen
39	chr10:18949800-18951200	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr10:18949800-18951400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr10:18949800-18951600	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr10:18949800-18952200	Enhancers	Small Intestine	intestine
43	chr10:18949800-18956600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr10:18950000-18950800	Flanking Active TSS	Fetal Heart	heart
45	chr10:18950000-18950800	Flanking Active TSS	Fetal Lung	lung
46	chr10:18950000-18951000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr10:18950000-18951000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr10:18950000-18951000	Enhancers	Placenta Amnion	Placenta Amnion
49	chr10:18950000-18951000	Enhancers	Thymus	Thymus
50	chr10:18950000-18951200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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