Variant report

Variant	rs6573547
Chromosome Location	chr14:64665994-64665995
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:64664909..64666611-chr14:64732886..64734717,2	MCF-7	breast:
2	chr14:64662559..64666637-chr14:64681435..64684914,4	MCF-7	breast:
3	chr14:64657113..64659774-chr14:64664998..64667785,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10162323	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1152590	0.84[CEU][hapmap];0.85[MEX][hapmap]
rs1152592	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs1152594	0.84[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs1152601	0.87[CEU][hapmap]
rs12435376	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1255990	0.85[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs1262242	0.85[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap]
rs1953234	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2027094	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]
rs2256191	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2776607	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2781379	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781380	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2987983	0.85[MEX][hapmap]
rs6573548	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7148072	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]
rs7148637	0.84[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs872227	0.85[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap]
rs968257	0.84[CEU][hapmap];0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6573547	MTHFD1	cis	cerebellum	SCAN
rs6573547	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs6573547	KCNH5	cis	parietal	SCAN
rs6573547	MTHFD1	cis	parietal	SCAN
rs6573547	SYNE2	cis	multi-tissue	Pritchard

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	chr14:64660800-64682600	Weak transcription	Hela-S3	cervix
6	chr14:64661600-64667000	Weak transcription	HepG2	liver
7	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:64661800-64675400	Weak transcription	NHEK	skin
10	chr14:64661800-64675600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr14:64662400-64675200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr14:64662800-64667400	Weak transcription	Lung	lung
13	chr14:64662800-64674800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr14:64663200-64667400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr14:64663800-64668600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr14:64664000-64667000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr14:64664000-64667000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr14:64664000-64667200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr14:64664000-64667400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr14:64664000-64668000	Weak transcription	Spleen	Spleen
21	chr14:64664000-64699600	Weak transcription	Small Intestine	intestine
22	chr14:64664200-64666200	Enhancers	Fetal Thymus	thymus
23	chr14:64664200-64666400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr14:64664200-64666600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr14:64664200-64666600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr14:64664200-64666600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr14:64664200-64666600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr14:64664200-64666600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr14:64664200-64666600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr14:64664200-64666600	Weak transcription	Fetal Intestine Small	intestine
31	chr14:64664200-64666600	Weak transcription	Placenta	Placenta
32	chr14:64664200-64666800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr14:64664200-64666800	Weak transcription	Fetal Stomach	stomach
34	chr14:64664200-64666800	Weak transcription	K562	blood
35	chr14:64664200-64667000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr14:64664200-64667000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr14:64664200-64667000	Weak transcription	Fetal Muscle Leg	muscle
38	chr14:64664200-64667200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr14:64664200-64668600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr14:64664200-64675000	Weak transcription	Aorta	Aorta
41	chr14:64664200-64675000	Weak transcription	Colonic Mucosa	Colon
42	chr14:64664200-64675400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr14:64664200-64676200	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr14:64664200-64698600	Weak transcription	HMEC	breast
45	chr14:64664400-64666400	Enhancers	Fetal Heart	heart
46	chr14:64664400-64666600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr14:64664400-64666600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr14:64664400-64666600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr14:64664400-64666600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr14:64664400-64666600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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