Variant report

Variant	rs2027094
Chromosome Location	chr14:64664758-64664759
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr14:64662665-64665717	H1-neurons	neurons:	n/a	chr14:64663684-64663704 chr14:64663869-64663878 chr14:64663684-64663704 chr14:64663684-64663704 chr14:64663726-64663739
2	MXI1	chr14:64663169-64664777	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64662559..64666637-chr14:64681435..64684914,4	MCF-7	breast:
2	chr14:64660992..64662814-chr14:64664224..64665884,2	MCF-7	breast:

Variant related genes	Relation type
SYNE2	TF binding region
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10143616	0.84[JPT][hapmap]
rs10162323	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1152590	0.90[CEU][hapmap]
rs1152592	0.90[CEU][hapmap]
rs1152594	0.90[CEU][hapmap]
rs1152601	0.90[CEU][hapmap]
rs12435376	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1255990	0.90[CEU][hapmap]
rs1255992	0.80[EUR][1000 genomes]
rs1262242	0.90[CEU][hapmap]
rs1953234	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2256191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2776607	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2781379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781380	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6573547	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6573548	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7148072	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7148637	0.86[EUR][1000 genomes]
rs872227	0.90[CEU][hapmap]
rs968257	0.95[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv902021	chr14:64647646-64715794	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2027094	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs2027094	ESR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64600600-64667400	Weak transcription	Stomach Mucosa	stomach
2	chr14:64650800-64671800	Strong transcription	Liver	Liver
3	chr14:64652800-64666200	Strong transcription	Dnd41	blood
4	chr14:64658200-64667000	Weak transcription	Esophagus	oesophagus
5	chr14:64660600-64665200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr14:64660800-64682600	Weak transcription	Hela-S3	cervix
7	chr14:64661600-64667000	Weak transcription	HepG2	liver
8	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr14:64661800-64675400	Weak transcription	NHEK	skin
11	chr14:64661800-64675600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr14:64662400-64675200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr14:64662600-64665400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr14:64662800-64665600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr14:64662800-64667400	Weak transcription	Lung	lung
16	chr14:64662800-64674800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr14:64663200-64665200	Active TSS	Brain Angular Gyrus	brain
18	chr14:64663200-64665400	Active TSS	Brain Anterior Caudate	brain
19	chr14:64663200-64667400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr14:64663400-64664800	Active TSS	Brain Cingulate Gyrus	brain
21	chr14:64663400-64664800	Active TSS	Right Atrium	heart
22	chr14:64663800-64665400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr14:64663800-64668600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr14:64664000-64665000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr14:64664000-64665000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr14:64664000-64665200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr14:64664000-64665800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr14:64664000-64665800	Weak transcription	Gastric	stomach
29	chr14:64664000-64667000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr14:64664000-64667000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr14:64664000-64667200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr14:64664000-64667400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr14:64664000-64668000	Weak transcription	Spleen	Spleen
34	chr14:64664000-64699600	Weak transcription	Small Intestine	intestine
35	chr14:64664200-64664800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr14:64664200-64665000	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr14:64664200-64665000	Weak transcription	Left Ventricle	heart
38	chr14:64664200-64665000	Active TSS	Thymus	Thymus
39	chr14:64664200-64665200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr14:64664200-64665200	Weak transcription	Pancreas	Pancrea
41	chr14:64664200-64665200	Weak transcription	Right Ventricle	heart
42	chr14:64664200-64665200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr14:64664200-64665400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr14:64664200-64665400	Weak transcription	Psoas Muscle	Psoas
45	chr14:64664200-64665600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr14:64664200-64666200	Enhancers	Fetal Thymus	thymus
47	chr14:64664200-64666400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr14:64664200-64666600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr14:64664200-64666600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr14:64664200-64666600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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