Variant report

Variant	rs17102087
Chromosome Location	chr1:46727304-46727305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46727238..46734645-chr1:46735437..46741548,13	K562	blood:
2	chr1:46711538..46715530-chr1:46724242..46729029,6	K562	blood:
3	chr1:46724735..46727744-chr1:46766521..46769175,3	K562	blood:

Variant related genes	Relation type
ENSG00000132128	Chromatin interaction
ENSG00000085999	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10489770	0.81[CHD][hapmap]
rs10890386	0.81[MEX][hapmap]
rs10890388	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs12125573	0.94[JPT][hapmap];0.86[MEX][hapmap]
rs12141269	0.89[CHB][hapmap]
rs12406217	0.89[CHB][hapmap]
rs1547180	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs4660918	0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4660919	0.94[JPT][hapmap]
rs4660920	0.94[JPT][hapmap]
rs4660921	0.94[JPT][hapmap]
rs6689182	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17102087	FOXD2	cis	cerebellum	SCAN
rs17102087	CYP4Z1	cis	parietal	SCAN
rs17102087	CLDN19	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46713600-46743600	Weak transcription	Aorta	Aorta
2	chr1:46713800-46743400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:46714000-46731800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:46714200-46729200	Weak transcription	Placenta	Placenta
5	chr1:46714200-46743200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:46714200-46743400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:46714200-46743400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:46714200-46743600	Weak transcription	Gastric	stomach
9	chr1:46714200-46743800	Weak transcription	Right Atrium	heart
10	chr1:46714400-46736200	Weak transcription	Fetal Lung	lung
11	chr1:46714400-46743400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:46714400-46745400	Weak transcription	Fetal Brain Male	brain
13	chr1:46714400-46745600	Weak transcription	Fetal Kidney	kidney
14	chr1:46714400-46754200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:46714600-46736400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:46714600-46748600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:46714600-46749600	Weak transcription	Fetal Heart	heart
18	chr1:46714800-46728400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:46714800-46748400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:46715000-46740800	Strong transcription	Fetal Stomach	stomach
21	chr1:46715000-46752800	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:46715200-46743400	Weak transcription	Spleen	Spleen
23	chr1:46715200-46748000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr1:46715200-46748400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:46715200-46764200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:46715400-46748200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:46715400-46748400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:46715400-46748400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:46715400-46753000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:46715400-46754200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:46715400-46763800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:46715400-46764400	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:46715400-46765600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:46716000-46749400	Strong transcription	Fetal Thymus	thymus
35	chr1:46716200-46742800	Strong transcription	K562	blood
36	chr1:46717200-46748000	Strong transcription	Thymus	Thymus
37	chr1:46718200-46749600	Strong transcription	Dnd41	blood
38	chr1:46719800-46743200	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:46720600-46750800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:46720800-46766400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:46721400-46745000	Strong transcription	HepG2	liver
42	chr1:46721600-46753800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:46721800-46735200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:46721800-46743000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:46721800-46744200	Weak transcription	Primary T cells from cord blood	blood
46	chr1:46721800-46750600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:46722800-46729200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:46723000-46727400	Strong transcription	NHEK	skin
49	chr1:46723000-46743400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:46723200-46734800	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links