Variant report

Variant	rs7148072
Chromosome Location	chr14:64670565-64670566
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	chr14:64669769..64672305-chr14:64678227..64680767,2	MCF-7	breast:
2	chr14:64667402..64671365-chr14:64674791..64677546,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10162323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1152590	0.88[CEU][hapmap];0.90[MEX][hapmap]
rs1152592	0.84[CEU][hapmap];0.90[MEX][hapmap]
rs1152594	0.88[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs1152601	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs12435376	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1255990	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs1262242	0.88[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap]
rs1953234	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2027094	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]
rs2256191	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2776607	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2781379	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2781380	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2987983	0.89[MEX][hapmap]
rs6573547	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6573548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7148637	0.83[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs872227	0.88[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap]
rs968257	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7148072	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs7148072	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs7148072	SYNE2	cis	multi-tissue	Pritchard
rs7148072	KCNH5	cis	parietal	SCAN
rs7148072	MTHFD1	cis	parietal	SCAN
rs7148072	MTHFD1	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64650800-64671800	Strong transcription	Liver	Liver
2	chr14:64660800-64682600	Weak transcription	Hela-S3	cervix
3	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr14:64661800-64675400	Weak transcription	NHEK	skin
6	chr14:64661800-64675600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr14:64662400-64675200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr14:64662800-64674800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr14:64664000-64699600	Weak transcription	Small Intestine	intestine
10	chr14:64664200-64675000	Weak transcription	Aorta	Aorta
11	chr14:64664200-64675000	Weak transcription	Colonic Mucosa	Colon
12	chr14:64664200-64675400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr14:64664200-64676200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr14:64664200-64698600	Weak transcription	HMEC	breast
15	chr14:64664400-64672800	Weak transcription	Fetal Kidney	kidney
16	chr14:64664400-64675800	Weak transcription	NHLF	lung
17	chr14:64664800-64672200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr14:64665000-64671000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr14:64665000-64672400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr14:64665000-64673800	Enhancers	Thymus	Thymus
21	chr14:64665000-64674800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr14:64665000-64675600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr14:64665200-64670800	Enhancers	Pancreas	Pancrea
24	chr14:64665200-64672000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr14:64665200-64676600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr14:64665400-64674800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr14:64665400-64675400	Weak transcription	Brain Anterior Caudate	brain
28	chr14:64665400-64700200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr14:64666000-64675200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr14:64666200-64674800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr14:64666200-64675400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr14:64666200-64675800	Weak transcription	Brain Angular Gyrus	brain
33	chr14:64666200-64678600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr14:64666200-64686000	Weak transcription	Brain Hippocampus Middle	brain
35	chr14:64666800-64699400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr14:64667000-64670800	Enhancers	Fetal Thymus	thymus
37	chr14:64667200-64675000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr14:64667200-64675000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr14:64667400-64670800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr14:64667400-64672200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr14:64667400-64674800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr14:64667400-64675000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr14:64667400-64679200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr14:64667400-64690200	Weak transcription	HepG2	liver
45	chr14:64667600-64672000	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr14:64667600-64674800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr14:64667600-64675200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr14:64667600-64676000	Weak transcription	Psoas Muscle	Psoas
49	chr14:64667600-64676000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr14:64667600-64686200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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