Variant report

Variant	rs9444486
Chromosome Location	chr6:87956454-87956455
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:87953694..87956480-chr6:87964610..87967479,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1145713	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1145714	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1145715	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1145716	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11759727	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1188806	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1203162	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1203163	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1203164	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12194354	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13201289	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16878497	0.85[EUR][1000 genomes]
rs1746444	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1753152	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs181491	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1925686	0.86[EUR][1000 genomes]
rs2025490	0.80[EUR][1000 genomes]
rs2236048	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2257153	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs242274	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs242275	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs242276	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs242282	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2983136	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs368267	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs374792	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs382956	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs384318	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs385210	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3857486	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3999791	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs411606	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs413687	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs414453	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4235830	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4707344	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4707345	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4707355	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62439540	0.80[EUR][1000 genomes]
rs6908834	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6913159	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6921673	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6926686	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6932641	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6938885	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6939075	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6940325	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7752414	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7757330	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7758360	0.84[ASN][1000 genomes]
rs827433	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs912815	0.86[EUR][1000 genomes]
rs9294375	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9294376	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444476	0.84[EUR][1000 genomes]
rs9444481	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444488	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9444490	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444491	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450619	0.80[EUR][1000 genomes]
rs9450623	0.85[EUR][1000 genomes]
rs9450630	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450636	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450637	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450638	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450639	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450640	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450646	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450651	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450653	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9444486	C6orf162	cis	multi-tissue	Pritchard
rs9444486	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9444486	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs9444486	C6orf162	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87884000-87964400	Weak transcription	NHEK	skin
2	chr6:87888200-87964200	Weak transcription	HSMMtube	muscle
3	chr6:87906400-87964400	Weak transcription	NHLF	lung
4	chr6:87923400-87969000	Weak transcription	Psoas Muscle	Psoas
5	chr6:87924400-87966000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:87934600-87964200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:87934600-87964400	Weak transcription	Brain Angular Gyrus	brain
8	chr6:87934600-87967000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:87934800-87958600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:87934800-87964200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:87935200-87963400	Weak transcription	Hela-S3	cervix
12	chr6:87935200-87963600	Weak transcription	NHDF-Ad	bronchial
13	chr6:87935800-87956800	Weak transcription	Osteobl	bone
14	chr6:87936400-87961600	Weak transcription	Right Atrium	heart
15	chr6:87936800-87964200	Weak transcription	Fetal Brain Male	brain
16	chr6:87946000-87964400	Weak transcription	Fetal Heart	heart
17	chr6:87948200-87961400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:87948800-87971200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:87949600-87961400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:87949600-87970200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:87949800-87958600	Strong transcription	Liver	Liver
22	chr6:87949800-87962000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:87950200-87958800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:87950200-87960200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr6:87950200-87960400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:87950200-87960400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr6:87950200-87962600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:87950200-87967600	Strong transcription	Fetal Lung	lung
29	chr6:87950200-87968200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr6:87950400-87959400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:87950400-87960400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:87950400-87970600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:87950400-87971400	Strong transcription	Dnd41	blood
34	chr6:87950600-87959600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:87950600-87964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:87950800-87964000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr6:87950800-87966000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:87951600-87964200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:87952200-87960200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr6:87952200-87964600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:87952200-87967600	Strong transcription	Primary hematopoietic stem cells	blood
42	chr6:87952600-87961000	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr6:87952800-87959000	Weak transcription	Fetal Brain Female	brain
44	chr6:87953000-87961400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:87953200-87960000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:87953400-87968200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:87953600-87959400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr6:87953800-87959200	Strong transcription	GM12878-XiMat	blood
49	chr6:87954200-87967600	Weak transcription	Stomach Mucosa	stomach
50	chr6:87954200-87970000	Strong transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links