Variant report

Variant	rs16859507
Chromosome Location	chr3:112084072-112084073
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10804500	0.81[EUR][1000 genomes]
rs10934166	0.81[EUR][1000 genomes]
rs10934167	0.81[EUR][1000 genomes]
rs10934169	0.81[EUR][1000 genomes]
rs10934170	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11708769	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710561	0.81[EUR][1000 genomes]
rs11712036	0.81[EUR][1000 genomes]
rs11719721	0.81[EUR][1000 genomes]
rs11917581	0.81[EUR][1000 genomes]
rs12629421	0.81[EUR][1000 genomes]
rs12630238	0.81[EUR][1000 genomes]
rs12630278	0.81[EUR][1000 genomes]
rs12633029	0.81[EUR][1000 genomes]
rs12634619	0.81[EUR][1000 genomes]
rs12635015	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12635872	0.90[EUR][1000 genomes]
rs16859469	0.81[EUR][1000 genomes]
rs1814987	0.81[EUR][1000 genomes]
rs1879511	0.81[EUR][1000 genomes]
rs1906520	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2895395	0.81[EUR][1000 genomes]
rs2895396	1.00[EUR][1000 genomes]
rs2971203	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4355253	0.81[EUR][1000 genomes]
rs4355254	0.81[EUR][1000 genomes]
rs57025230	0.81[EUR][1000 genomes]
rs57661530	0.86[EUR][1000 genomes]
rs58425909	0.81[EUR][1000 genomes]
rs59202208	0.81[EUR][1000 genomes]
rs59744939	0.81[EUR][1000 genomes]
rs60204227	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62264124	0.81[EUR][1000 genomes]
rs62278831	0.81[EUR][1000 genomes]
rs62278832	0.81[EUR][1000 genomes]
rs62278833	0.81[EUR][1000 genomes]
rs62278834	0.81[EUR][1000 genomes]
rs62278835	0.81[EUR][1000 genomes]
rs62278836	0.81[EUR][1000 genomes]
rs62278837	0.81[EUR][1000 genomes]
rs62278838	0.81[EUR][1000 genomes]
rs62278839	0.81[EUR][1000 genomes]
rs62278841	0.81[EUR][1000 genomes]
rs62278842	0.81[EUR][1000 genomes]
rs62278844	0.81[EUR][1000 genomes]
rs62278848	0.81[EUR][1000 genomes]
rs62278849	0.81[EUR][1000 genomes]
rs62278850	0.81[EUR][1000 genomes]
rs62278853	0.81[EUR][1000 genomes]
rs62278854	0.81[EUR][1000 genomes]
rs62278855	0.81[EUR][1000 genomes]
rs62278856	0.81[EUR][1000 genomes]
rs6764384	0.81[EUR][1000 genomes]
rs6787841	0.81[EUR][1000 genomes]
rs6788309	0.81[EUR][1000 genomes]
rs6789161	0.81[EUR][1000 genomes]
rs6801708	0.81[EUR][1000 genomes]
rs6801739	0.81[EUR][1000 genomes]
rs72950242	0.81[EUR][1000 genomes]
rs72950273	0.81[EUR][1000 genomes]
rs72952411	0.86[EUR][1000 genomes]
rs72952437	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952454	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72952463	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7653490	0.81[EUR][1000 genomes]
rs869042	0.81[EUR][1000 genomes]
rs9834347	0.82[EUR][1000 genomes]
rs9863371	0.86[EUR][1000 genomes]
rs9867245	1.00[EUR][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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv877341	chr3:112079277-112125521	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16859507	MTHFD1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112066000-112089800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:112069200-112095400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:112070200-112086200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:112070600-112086200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:112070600-112088800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:112070800-112084600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:112070800-112090600	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:112077200-112094200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:112077600-112107200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:112077800-112085400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:112077800-112085400	Weak transcription	Ovary	ovary
12	chr3:112078000-112085200	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:112078200-112086400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:112079400-112085600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:112079400-112085800	Strong transcription	Primary hematopoietic stem cells	blood
16	chr3:112079400-112086200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:112079600-112085800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:112080000-112088800	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:112080000-112096000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:112080600-112087400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:112080800-112084200	Weak transcription	Aorta	Aorta
22	chr3:112081000-112085600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:112081000-112088800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:112081200-112085400	Weak transcription	Brain Angular Gyrus	brain
25	chr3:112081200-112085800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:112081200-112092800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:112081400-112085400	Weak transcription	Fetal Brain Male	brain
28	chr3:112081400-112088000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:112081400-112091600	Weak transcription	Primary T cells from cord blood	blood
30	chr3:112082200-112096000	Weak transcription	Fetal Stomach	stomach
31	chr3:112082400-112084600	Strong transcription	Brain Germinal Matrix	brain
32	chr3:112082600-112084600	Strong transcription	Fetal Muscle Leg	muscle
33	chr3:112082600-112094600	Weak transcription	Brain Anterior Caudate	brain
34	chr3:112082800-112084800	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr3:112083000-112085600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:112083000-112085600	Enhancers	HMEC	breast
37	chr3:112083200-112084800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:112083200-112085000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr3:112083200-112085800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:112083200-112086000	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:112083400-112085400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:112083400-112086200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:112083400-112092200	Weak transcription	Primary B cells from cord blood	blood
44	chr3:112083600-112084400	Enhancers	Placenta	Placenta
45	chr3:112083600-112084800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:112083600-112085000	Strong transcription	Thymus	Thymus
47	chr3:112083600-112085000	Enhancers	NHEK	skin
48	chr3:112083600-112085400	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr3:112083600-112085600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:112083600-112085800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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