Variant report

Variant	rs16917628
Chromosome Location	chr10:18951348-18951349
allele	C/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	CHD1	chr10:18946884-18951792	IMR90	lung:	n/a	chr10:18948546-18948556 chr10:18948735-18948745
2	POLR2A	chr10:18949923-18951350	HepG2	liver:	n/a	n/a
3	POLR2A	chr10:18946803-18951639	IMR90	lung:	n/a	n/a
4	POLR2A	chr10:18950080-18951470	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	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: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10466095	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10508564	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11014651	0.85[YRI][hapmap]
rs11014769	1.00[YRI][hapmap]
rs11014986	0.93[YRI][hapmap]
rs11014994	0.94[AFR][1000 genomes]
rs11015019	0.97[AFR][1000 genomes]
rs11015036	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs11015184	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs11015254	0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015323	0.93[YRI][hapmap]
rs11015443	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11498244	0.85[AFR][1000 genomes]
rs12243188	0.93[YRI][hapmap]
rs12246317	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12246433	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12247548	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12247869	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12249604	0.87[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12250601	0.89[AFR][1000 genomes]
rs12255014	0.82[AFR][1000 genomes]
rs12258306	0.89[AFR][1000 genomes]
rs12258688	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12267659	0.92[AFR][1000 genomes]
rs12269605	0.92[AFR][1000 genomes]
rs16917423	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap]
rs16917589	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs16917615	0.93[YRI][hapmap];0.97[AFR][1000 genomes]
rs17363677	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs28794621	0.83[AMR][1000 genomes]
rs4614337	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7088674	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7100918	0.95[AFR][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	chr10:18947400-18951600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr10:18949000-18954000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:18949400-18951400	Flanking Active TSS	Dnd41	blood
4	chr10:18949400-18973200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:18949600-18951400	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr10:18949600-18951400	Enhancers	Brain Hippocampus Middle	brain
7	chr10:18949600-18951400	Enhancers	Colon Smooth Muscle	Colon
8	chr10:18949600-18951400	Enhancers	Fetal Brain Male	brain
9	chr10:18949600-18951600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr10:18949600-18951800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr10:18949600-18952400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr10:18949600-18952400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr10:18949600-18953800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr10:18949600-18957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr10:18949600-18972000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr10:18949800-18951400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr10:18949800-18951600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr10:18949800-18952200	Enhancers	Small Intestine	intestine
19	chr10:18949800-18956600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr10:18950000-18953800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr10:18950000-18956600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr10:18950000-18957600	Weak transcription	Fetal Stomach	stomach
23	chr10:18950200-18951400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr10:18950200-18951400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr10:18950200-18953600	Weak transcription	Lung	lung
26	chr10:18950200-18954600	Weak transcription	HSMM	muscle
27	chr10:18950200-18956000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:18950200-18956800	Weak transcription	Left Ventricle	heart
29	chr10:18950200-18957000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr10:18950200-18957000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr10:18950200-18957600	Weak transcription	Placenta	Placenta
32	chr10:18950400-18951400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr10:18950400-18951400	Weak transcription	HSMMtube	muscle
34	chr10:18950400-18951600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr10:18950400-18951600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr10:18950400-18953400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr10:18950400-18957000	Weak transcription	Adipose Nuclei	Adipose
38	chr10:18950600-18951400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr10:18950600-18951400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr10:18950600-18951800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr10:18950800-18951400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr10:18950800-18951400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr10:18950800-18951400	Flanking Active TSS	HepG2	liver
44	chr10:18950800-18951600	Enhancers	Fetal Heart	heart
45	chr10:18950800-18952200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr10:18950800-18953600	Weak transcription	Ovary	ovary
47	chr10:18950800-18954000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr10:18950800-18954000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr10:18950800-18954000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr10:18950800-18954200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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