Variant report

Variant	rs927220
Chromosome Location	chr14:68767972-68767973
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68767111..68768962-chr14:69260307..69262756,4	MCF-7	breast:
2	chr14:68714804..68718493-chr14:68766094..68768941,3	MCF-7	breast:
3	chr14:68764415..68769564-chr14:68770855..68774967,6	MCF-7	breast:
4	chr14:68765970..68770223-chr14:69260401..69262573,5	MCF-7	breast:
5	chr14:68760897..68764007-chr14:68767297..68769142,3	K562	blood:

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10083393	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10131654	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10135678	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10136039	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10144669	0.90[CEU][hapmap];0.96[YRI][hapmap];0.96[EUR][1000 genomes]
rs10483807	0.90[GIH][hapmap]
rs11158728	1.00[GIH][hapmap]
rs11158730	0.90[GIH][hapmap]
rs11621881	0.94[EUR][1000 genomes]
rs11627646	1.00[GIH][hapmap]
rs12880109	0.88[GIH][hapmap]
rs12890124	1.00[GIH][hapmap]
rs12892777	0.90[GIH][hapmap]
rs1956523	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1956526	0.85[GIH][hapmap]
rs1956528	1.00[GIH][hapmap]
rs1956529	1.00[GIH][hapmap]
rs1956532	1.00[GIH][hapmap]
rs2013413	0.90[GIH][hapmap]
rs2064912	1.00[GIH][hapmap]
rs2064914	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2145423	1.00[GIH][hapmap]
rs3784104	1.00[GIH][hapmap]
rs3784106	0.95[CEU][hapmap];0.88[GIH][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes]
rs3784108	1.00[GIH][hapmap]
rs4410007	0.96[EUR][1000 genomes]
rs4899238	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4902566	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7147852	1.00[GIH][hapmap]
rs7148322	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7148412	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7149396	0.85[GIH][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.94[EUR][1000 genomes]
rs7150988	1.00[GIH][hapmap]
rs7151629	0.88[ASW][hapmap];0.95[CEU][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7493547	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs8013078	0.95[CEU][hapmap];0.93[YRI][hapmap];0.97[EUR][1000 genomes]
rs8013968	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs8017304	1.00[GIH][hapmap]
rs8022860	0.97[EUR][1000 genomes]
rs911254	0.90[GIH][hapmap]
rs911255	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs911258	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9323506	0.90[EUR][1000 genomes]
rs9989152	0.95[CEU][hapmap];0.96[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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv428628	chr14:68674504-68835127	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs927220	MTHFD1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68752400-68768800	Weak transcription	Aorta	Aorta
2	chr14:68753400-68768800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr14:68753600-68768600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr14:68753600-68768800	Weak transcription	Dnd41	blood
5	chr14:68759000-68768400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:68760000-68768800	Weak transcription	Thymus	Thymus
7	chr14:68760400-68768800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr14:68760400-68776800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr14:68760600-68768400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr14:68760600-68768600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr14:68760600-68773600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr14:68762000-68773400	Weak transcription	Small Intestine	intestine
13	chr14:68762800-68768800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:68762800-68771400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr14:68763000-68768800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr14:68763400-68768400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr14:68763400-68772400	Weak transcription	Pancreas	Pancrea
18	chr14:68763800-68768800	Weak transcription	Primary B cells from cord blood	blood
19	chr14:68765000-68774600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr14:68765200-68771000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr14:68765400-68768600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr14:68765400-68768600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr14:68765600-68768400	Weak transcription	Fetal Thymus	thymus
24	chr14:68765600-68768800	Weak transcription	Fetal Muscle Leg	muscle
25	chr14:68766400-68768000	Enhancers	Fetal Heart	heart
26	chr14:68767400-68768200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr14:68767400-68768200	Enhancers	Fetal Stomach	stomach
28	chr14:68767400-68768200	Enhancers	Ovary	ovary
29	chr14:68767600-68768400	Enhancers	Fetal Lung	lung
30	chr14:68767600-68768600	Enhancers	Fetal Intestine Small	intestine
31	chr14:68767600-68776400	Weak transcription	Left Ventricle	heart
32	chr14:68767800-68768000	Enhancers	Fetal Intestine Large	intestine
33	chr14:68767800-68768400	Weak transcription	A549	lung

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