Variant report

Variant	rs4150909
Chromosome Location	chr8:86107836-86107837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86088335..86091633-chr8:86107485..86113075,5	MCF-7	breast:
2	chr8:86106829..86109300-chr8:86133034..86134778,2	K562	blood:

Variant related genes	Relation type
ENSG00000254208	Chromatin interaction
ENSG00000133740	Chromatin interaction
ENSG00000260493	Chromatin interaction
ENSG00000185015	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10088120	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs10090196	0.86[JPT][hapmap]
rs10091577	0.82[ASN][1000 genomes]
rs10091710	0.81[ASN][1000 genomes]
rs10100442	0.95[JPT][hapmap]
rs10106970	0.86[ASN][1000 genomes]
rs1021583	0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11261468	0.91[JPT][hapmap]
rs11261471	0.83[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs12541445	0.83[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs12543256	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12544332	0.86[JPT][hapmap]
rs12546106	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs12550160	0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1303806	0.82[JPT][hapmap]
rs13259399	0.86[JPT][hapmap]
rs13269739	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1390711	0.82[JPT][hapmap]
rs1496531	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1496532	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1553015	0.82[JPT][hapmap]
rs16913681	0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs16913721	0.86[JPT][hapmap];0.84[MEX][hapmap]
rs17740658	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs1845891	0.81[ASN][1000 genomes]
rs1845892	0.84[ASN][1000 genomes]
rs1908762	0.83[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs1995057	0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs1995058	0.82[JPT][hapmap];0.84[TSI][hapmap]
rs2006767	0.81[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs2132589	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2132590	0.82[ASN][1000 genomes]
rs2278459	0.91[JPT][hapmap]
rs2279701	0.91[JPT][hapmap]
rs2291786	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs2291787	0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs2403083	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2403084	0.95[ASN][1000 genomes]
rs2403085	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2403086	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2403088	0.91[JPT][hapmap]
rs2403104	0.82[JPT][hapmap]
rs28377260	0.82[ASN][1000 genomes]
rs28439950	0.84[ASN][1000 genomes]
rs28564613	0.84[ASN][1000 genomes]
rs2896452	0.91[JPT][hapmap]
rs2896454	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs34103685	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs34527380	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3779899	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs3779901	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3808538	0.86[JPT][hapmap]
rs3808539	0.82[JPT][hapmap];0.82[TSI][hapmap]
rs4150865	0.82[ASN][1000 genomes]
rs4150867	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4150868	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4150869	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4150884	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4150893	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs4150897	0.94[ASN][1000 genomes]
rs4150942	0.91[JPT][hapmap];0.84[MEX][hapmap]
rs4150944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4150962	0.88[ASN][1000 genomes]
rs4150964	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs4150974	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs4150977	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs4609189	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4617148	0.81[ASN][1000 genomes]
rs4739698	0.84[ASN][1000 genomes]
rs4739700	0.86[JPT][hapmap]
rs4740043	0.85[JPT][hapmap]
rs4740044	0.86[JPT][hapmap]
rs4740045	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs4740047	0.81[ASN][1000 genomes]
rs4740049	0.82[JPT][hapmap]
rs62527173	0.82[ASN][1000 genomes]
rs6605610	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6605611	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6605624	0.90[JPT][hapmap]
rs6990449	0.86[JPT][hapmap]
rs6993316	0.81[ASN][1000 genomes]
rs6993387	0.86[JPT][hapmap]
rs6994113	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs7001359	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7008772	0.86[JPT][hapmap]
rs7011001	0.84[ASN][1000 genomes]
rs7011926	0.82[JPT][hapmap]
rs7015758	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7818163	0.86[JPT][hapmap]
rs7821629	0.85[ASN][1000 genomes]
rs7826589	0.85[JPT][hapmap]
rs7827175	0.83[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs7829050	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7829144	0.91[JPT][hapmap]
rs7829240	0.86[ASN][1000 genomes]
rs7839129	0.82[ASN][1000 genomes]
rs7841142	0.91[JPT][hapmap]
rs7842013	0.82[ASN][1000 genomes]
rs903895	0.82[JPT][hapmap];0.84[TSI][hapmap]
rs903896	0.82[JPT][hapmap]
rs903897	0.82[JPT][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	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv971329	chr8:86094967-86183119	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4150909	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs4150909	C8orf59	cis	cerebellum	SCAN
rs4150909	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs4150909	LRRCC1	cis	Esophagus Mucosa	GTEx
rs4150909	C8orf59	cis	parietal	SCAN
rs4150909	CA13	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86090800-86127800	Weak transcription	Aorta	Aorta
2	chr8:86091000-86127800	Weak transcription	HSMMtube	muscle
3	chr8:86091000-86132000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:86091200-86125200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr8:86091600-86110000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr8:86091600-86124200	Weak transcription	Primary T cells from cord blood	blood
7	chr8:86091600-86126000	Weak transcription	Hela-S3	cervix
8	chr8:86091800-86124200	Weak transcription	HMEC	breast
9	chr8:86096200-86108400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr8:86096200-86121400	Weak transcription	Fetal Lung	lung
11	chr8:86096400-86121400	Weak transcription	A549	lung
12	chr8:86096600-86120600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr8:86096800-86109600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr8:86096800-86113000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr8:86098000-86112800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr8:86100400-86121400	Weak transcription	Fetal Intestine Large	intestine
17	chr8:86101000-86122600	Weak transcription	Fetal Intestine Small	intestine
18	chr8:86101000-86124600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr8:86101000-86127800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr8:86101200-86127800	Weak transcription	Spleen	Spleen
21	chr8:86101200-86131000	Weak transcription	HepG2	liver
22	chr8:86102600-86108800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr8:86102600-86108800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr8:86102600-86112800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr8:86102600-86113600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr8:86102600-86121000	Weak transcription	Fetal Muscle Leg	muscle
27	chr8:86102600-86121600	Weak transcription	Dnd41	blood
28	chr8:86102600-86125000	Weak transcription	Fetal Stomach	stomach
29	chr8:86102600-86125200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr8:86102600-86128200	Weak transcription	Fetal Brain Male	brain
31	chr8:86102800-86112800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr8:86103200-86113000	Weak transcription	Fetal Thymus	thymus
33	chr8:86103200-86118400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr8:86103200-86120800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr8:86103600-86108600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr8:86104000-86113200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr8:86106000-86108800	Enhancers	Primary B cells from cord blood	blood
38	chr8:86106000-86110000	Weak transcription	GM12878-XiMat	blood
39	chr8:86106000-86112800	Weak transcription	Right Ventricle	heart
40	chr8:86106000-86120800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr8:86106200-86112800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr8:86106800-86108000	Enhancers	Primary B cells from peripheral blood	blood
43	chr8:86106800-86108000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr8:86107200-86112400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr8:86107600-86108000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr8:86107800-86108200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr8:86107800-86108600	Enhancers	Primary hematopoietic stem cells	blood
48	chr8:86107800-86110400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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