Variant report

Variant	rs4418736
Chromosome Location	chr10:99179206-99179207
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:6)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99167329..99170303-chr10:99178953..99180930,2	K562	blood:
2	chr10:99174155..99176594-chr10:99178151..99179962,2	MCF-7	breast:
3	chr10:99178412..99183286-chr10:99183902..99188289,4	K562	blood:
4	chr10:99158317..99161416-chr10:99176559..99179777,3	K562	blood:
5	chr10:99171315..99175453-chr10:99176654..99180468,6	K562	blood:
6	chr10:99176991..99182775-chr10:99183273..99189892,9	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL355490.1-1	chr10:99178541-99179252	XLOC_008916
2	lnc-PGAM1-1	chr10:99179059-99179327	XLOC_008574
3	lnc-AL355490.1-1	chr10:99176179-99185666	NONHSAT015863

No data

Variant related genes	Relation type
ENSG00000224474	Chromatin interaction
ENSG00000231970	Chromatin interaction
ENSG00000171314	Chromatin interaction
ENSG00000052749	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10882935	0.82[ASN][1000 genomes]
rs11189213	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs11189254	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12245837	0.82[JPT][hapmap]
rs12259524	0.82[JPT][hapmap]
rs1253398	0.85[MEX][hapmap]
rs1253406	0.85[MEX][hapmap]
rs17107905	0.91[CHD][hapmap];0.82[JPT][hapmap]
rs17108072	0.82[JPT][hapmap]
rs17112598	0.82[MEX][hapmap]
rs17112803	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs17557994	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1889545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2253301	0.85[MEX][hapmap]
rs2297990	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28362478	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2861953	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3763672	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3814552	0.91[CHD][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs3893064	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41300215	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41300217	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41303833	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4917767	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4917769	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4919088	1.00[MEX][hapmap]
rs4919095	0.81[EUR][1000 genomes]
rs4919098	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4919110	0.82[JPT][hapmap]
rs59058784	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60305070	0.81[EUR][1000 genomes]
rs60890987	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs701822	0.85[MEX][hapmap]
rs7089713	0.84[CHD][hapmap]
rs793514	0.85[MEX][hapmap]
rs793529	0.85[MEX][hapmap]
rs928604	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs946984	0.82[JPT][hapmap]
rs946987	0.84[CHD][hapmap]
rs964733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467440	chr10:99134784-99204791	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv552025	chr10:99134784-99204791	Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4418736	GALNT9	trans	lymphoblastoid	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99161600-99185200	Weak transcription	Pancreas	Pancrea
2	chr10:99167400-99185200	Weak transcription	Fetal Lung	lung
3	chr10:99167400-99185400	Weak transcription	Gastric	stomach
4	chr10:99167600-99185200	Weak transcription	Fetal Intestine Small	intestine
5	chr10:99167600-99185200	Weak transcription	Left Ventricle	heart
6	chr10:99171400-99179400	Weak transcription	Spleen	Spleen
7	chr10:99171400-99185200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:99173200-99182800	Weak transcription	HUVEC	blood vessel
9	chr10:99173800-99182400	Weak transcription	Esophagus	oesophagus
10	chr10:99174000-99185000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:99174200-99183000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr10:99174200-99184800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:99174200-99185000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr10:99175000-99182800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:99175200-99182200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:99175200-99182800	Weak transcription	NH-A	brain
17	chr10:99175200-99182800	Weak transcription	Osteobl	bone
18	chr10:99175400-99185000	Weak transcription	Brain Germinal Matrix	brain
19	chr10:99176600-99183000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr10:99176600-99185200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr10:99177800-99179800	Enhancers	Fetal Thymus	thymus
22	chr10:99177800-99185200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr10:99178000-99179400	Enhancers	Primary hematopoietic stem cells	blood
24	chr10:99178000-99179400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr10:99178000-99179400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr10:99178000-99179800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr10:99178200-99179400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr10:99178200-99185200	Weak transcription	Ovary	ovary
29	chr10:99178400-99180400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr10:99178400-99180800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr10:99178400-99185000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr10:99178400-99185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:99178400-99185200	Weak transcription	Right Ventricle	heart
34	chr10:99178400-99185200	Weak transcription	Small Intestine	intestine
35	chr10:99178600-99179600	Enhancers	Primary B cells from cord blood	blood
36	chr10:99178600-99179600	Enhancers	Fetal Muscle Trunk	muscle
37	chr10:99178600-99184800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr10:99178800-99179400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr10:99178800-99179400	Flanking Active TSS	K562	blood
40	chr10:99178800-99182800	Weak transcription	GM12878-XiMat	blood
41	chr10:99178800-99185400	Weak transcription	Aorta	Aorta
42	chr10:99179000-99179400	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr10:99179000-99179400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr10:99179000-99179400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr10:99179000-99179400	Enhancers	Thymus	Thymus
46	chr10:99179000-99179600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr10:99179000-99179800	Enhancers	HSMMtube	muscle
48	chr10:99179000-99184800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr10:99179000-99184800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr10:99179000-99185200	Weak transcription	Lung	lung

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