Variant report

Variant	rs6809499
Chromosome Location	chr3:56687093-56687094
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	chr3:56685409..56688406-chr3:56693348..56695126,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10049468	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11130537	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130540	0.90[EUR][1000 genomes]
rs11130541	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17235670	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2317134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2317244	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2317252	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs282522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs282523	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs282528	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282536	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs282541	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4234393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4681725	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4681734	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4681740	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4681933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681964	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4681980	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682000	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55831745	0.88[ASN][1000 genomes]
rs55938093	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56190096	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56204053	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62251242	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445801	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445803	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445804	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445809	0.85[AMR][1000 genomes]
rs6445810	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6778373	0.88[ASN][1000 genomes]
rs6781056	0.88[ASN][1000 genomes]
rs6781293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[ASN][1000 genomes]
rs6787227	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs6802498	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73079883	0.82[ASN][1000 genomes]
rs73079884	0.82[ASN][1000 genomes]
rs73079891	0.82[ASN][1000 genomes]
rs73079902	0.88[ASN][1000 genomes]
rs73081810	0.88[ASN][1000 genomes]
rs73081811	0.88[ASN][1000 genomes]
rs73081819	0.88[ASN][1000 genomes]
rs73081823	0.88[ASN][1000 genomes]
rs73081825	0.88[ASN][1000 genomes]
rs73081851	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081854	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617331	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7618007	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7619465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7620259	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7631662	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7637449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7642389	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9809309	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9833926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9835332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9839065	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9851653	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9858568	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9875257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs9878373	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6809499	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL
rs6809499	CCDC66	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:56647400-56707400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:56647400-56707800	Strong transcription	Fetal Thymus	thymus
7	chr3:56651400-56702000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:56652800-56701400	Weak transcription	Psoas Muscle	Psoas
9	chr3:56661400-56710600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:56664000-56688000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:56664000-56694800	Weak transcription	Stomach Mucosa	stomach
12	chr3:56664800-56687400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr3:56664800-56711000	Strong transcription	Dnd41	blood
14	chr3:56665000-56687800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:56665000-56690400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:56665000-56707800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:56665200-56691800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:56665200-56698800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr3:56665200-56707200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:56665800-56687400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:56665800-56687400	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:56666200-56708000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr3:56668000-56688600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:56668000-56707200	Strong transcription	Placenta	Placenta
25	chr3:56669600-56703800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:56673600-56687600	Strong transcription	GM12878-XiMat	blood
27	chr3:56675600-56702200	Weak transcription	K562	blood
28	chr3:56675800-56687600	Weak transcription	Brain Anterior Caudate	brain
29	chr3:56675800-56687600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:56675800-56688600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:56675800-56688800	Weak transcription	Aorta	Aorta
32	chr3:56675800-56691600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:56675800-56691600	Weak transcription	HSMMtube	muscle
34	chr3:56675800-56691800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:56675800-56692400	Weak transcription	Right Ventricle	heart
36	chr3:56675800-56693400	Weak transcription	Colonic Mucosa	Colon
37	chr3:56675800-56695200	Weak transcription	Gastric	stomach
38	chr3:56675800-56707000	Weak transcription	Esophagus	oesophagus
39	chr3:56675800-56716200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:56676000-56705600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:56677000-56696600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:56677200-56705400	Strong transcription	Primary T cells from cord blood	blood
43	chr3:56677800-56688000	Strong transcription	Primary hematopoietic stem cells	blood
44	chr3:56678000-56690200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:56678200-56690400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:56678400-56690000	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr3:56678400-56690200	Strong transcription	Primary B cells from cord blood	blood
48	chr3:56678800-56687400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:56679000-56688600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:56680400-56687400	Weak transcription	Brain Hippocampus Middle	brain

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