Variant report

Variant	rs1981237
Chromosome Location	chr10:99519097-99519098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99518900..99519671-chr10:99626991..99627760,2	K562	blood:
2	chr10:99518884..99519909-chr10:99628931..99629825,9	K562	blood:
3	chr10:99517904..99520050-chr10:99530268..99531843,2	K562	blood:
4	chr10:99518917..99520063-chr10:99628884..99629827,7	MCF-7	breast:
5	chr10:99518980..99521105-chr10:99786683..99789555,3	MCF-7	breast:
6	chr10:99518935..99521732-chr10:99573447..99575907,2	K562	blood:
7	chr10:99514392..99517245-chr10:99518332..99520439,2	MCF-7	breast:
8	chr10:99518931..99519801-chr10:99628905..99629856,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000155256	Chromatin interaction
ENSG00000120057	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10748708	0.86[ASN][1000 genomes]
rs10748709	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10786367	0.85[CEU][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs10786370	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs10786371	0.82[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs10786372	0.83[JPT][hapmap]
rs10786373	0.92[ASN][1000 genomes]
rs10786374	0.84[EUR][1000 genomes]
rs10882993	0.80[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs10882995	0.94[CEU][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs10882996	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10882997	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10882998	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs11189353	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs11189355	0.94[CEU][hapmap];0.80[JPT][hapmap]
rs11189357	0.94[CEU][hapmap];0.85[JPT][hapmap]
rs11189359	0.94[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap]
rs11189360	1.00[CEU][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11189361	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189362	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189367	0.82[EUR][1000 genomes]
rs11189374	0.83[EUR][1000 genomes]
rs11189377	0.83[EUR][1000 genomes]
rs12412543	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1253027	0.81[CHD][hapmap]
rs12569711	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12783992	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1556971	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1981238	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2010732	0.84[ASN][1000 genomes]
rs2027376	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2039826	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs34283185	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3750612	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3750614	0.80[CEU][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs3750615	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs3814558	0.80[CEU][hapmap];0.84[JPT][hapmap]
rs3814559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244329	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244330	0.89[EUR][1000 genomes]
rs4917784	0.82[JPT][hapmap]
rs4917786	0.87[ASN][1000 genomes]
rs4919139	0.83[CEU][hapmap];0.91[CHB][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7072751	0.90[ASN][1000 genomes]
rs7080894	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7080953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7081652	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7094519	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7099540	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7100453	0.84[EUR][1000 genomes]
rs7478323	0.90[EUR][1000 genomes]
rs7907679	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs7910589	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7916164	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7916454	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs7916593	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7922907	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs883324	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs946777	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs946778	0.80[CEU][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]

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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1981237	ZFYVE27	cis	parietal	SCAN
rs1981237	DHDPSL	cis	cerebellum	SCAN
rs1981237	ZFYVE27	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99497600-99522600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:99498200-99520600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:99498400-99519200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr10:99498600-99520200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:99498600-99520600	Strong transcription	Osteobl	bone
6	chr10:99498600-99522200	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr10:99498600-99522400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr10:99498600-99522400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr10:99498600-99523000	Strong transcription	Thymus	Thymus
10	chr10:99498600-99523600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr10:99498600-99524800	Weak transcription	Fetal Brain Male	brain
12	chr10:99498800-99522400	Strong transcription	Dnd41	blood
13	chr10:99499200-99522800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr10:99499200-99523400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr10:99499400-99522000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr10:99499400-99522400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:99499600-99519200	Strong transcription	Placenta	Placenta
18	chr10:99500000-99523000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr10:99500400-99522000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr10:99500600-99523200	Strong transcription	Brain Germinal Matrix	brain
21	chr10:99502000-99522800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr10:99502200-99522600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr10:99502400-99520000	Strong transcription	Primary B cells from cord blood	blood
24	chr10:99502600-99519200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr10:99502600-99522600	Strong transcription	Primary T cells from cord blood	blood
26	chr10:99502800-99521600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr10:99502800-99522600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr10:99503000-99524000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:99503400-99522200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr10:99503400-99522800	Strong transcription	Liver	Liver
31	chr10:99503600-99519200	Strong transcription	Adipose Nuclei	Adipose
32	chr10:99503600-99522400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr10:99504000-99520600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:99504200-99521800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr10:99504200-99523600	Strong transcription	Fetal Intestine Small	intestine
36	chr10:99504600-99522000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr10:99506400-99523000	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr10:99507000-99521200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr10:99507200-99519400	Strong transcription	Brain Cingulate Gyrus	brain
40	chr10:99507400-99522000	Strong transcription	Ovary	ovary
41	chr10:99508200-99522200	Weak transcription	Fetal Heart	heart
42	chr10:99509800-99522000	Weak transcription	Stomach Mucosa	stomach
43	chr10:99511200-99522000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr10:99514600-99521800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr10:99514800-99526600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:99515000-99522800	Weak transcription	Fetal Kidney	kidney
47	chr10:99515200-99523000	Strong transcription	Fetal Stomach	stomach
48	chr10:99515200-99523200	Strong transcription	Lung	lung
49	chr10:99515400-99526200	Weak transcription	NH-A	brain
50	chr10:99515600-99519200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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