Variant report

Variant	rs1152588
Chromosome Location	chr14:64688175-64688176
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64679731..64682814-chr14:64685372..64689145,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10148269	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10151658	0.87[YRI][hapmap]
rs1152577	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1152578	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1152579	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1152582	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1152586	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1152589	0.89[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1152590	0.84[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1152591	0.95[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1152592	0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1152593	0.83[ASN][1000 genomes]
rs1152594	0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1152601	0.83[CHB][hapmap]
rs1255984	0.89[CHB][hapmap];0.87[YRI][hapmap]
rs1255986	0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes]
rs1255988	0.86[AFR][1000 genomes]
rs1255990	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1256030	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1256036	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1256037	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1256038	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1256039	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1256041	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1256042	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1256043	0.91[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1256044	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1256045	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1256046	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1256048	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs1256056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1256059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1256065	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1262242	0.84[CHB][hapmap]
rs1266927	0.84[AFR][1000 genomes]
rs1269056	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1271573	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1760988	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2738413	0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3020445	0.88[CEU][hapmap]
rs7229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs872227	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs915057	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs928554	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs944046	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs944047	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs960069	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1050378	chr14:64686543-64703012	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv974346	chr14:64687936-64688734	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1152588	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1152588	SYNE2	cis	multi-tissue	Pritchard
rs1152588	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1152588	ESR2	cis	Skin Sun Exposed Lower leg	GTEx
rs1152588	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64664000-64699600	Weak transcription	Small Intestine	intestine
2	chr14:64664200-64698600	Weak transcription	HMEC	breast
3	chr14:64665400-64700200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr14:64666800-64699400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr14:64667400-64690200	Weak transcription	HepG2	liver
6	chr14:64672800-64696600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr14:64674600-64696000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr14:64674600-64696200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr14:64674600-64696400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr14:64674600-64699800	Strong transcription	Liver	Liver
11	chr14:64674800-64689000	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr14:64674800-64689000	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr14:64674800-64692400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr14:64674800-64692600	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr14:64674800-64692800	Strong transcription	Primary T cells from cord blood	blood
16	chr14:64674800-64695800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr14:64674800-64696000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr14:64674800-64696000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr14:64674800-64696000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr14:64674800-64696200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr14:64674800-64696200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr14:64674800-64696200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr14:64674800-64696400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr14:64674800-64696400	Strong transcription	Dnd41	blood
25	chr14:64674800-64696800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr14:64674800-64697600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr14:64674800-64698400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr14:64674800-64699000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr14:64674800-64700000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr14:64674800-64700600	Strong transcription	Fetal Intestine Large	intestine
31	chr14:64675000-64689000	Strong transcription	Aorta	Aorta
32	chr14:64675000-64696400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr14:64675000-64696400	Strong transcription	Brain Germinal Matrix	brain
34	chr14:64675200-64696400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr14:64675400-64689200	Strong transcription	Rectal Smooth Muscle	rectum
36	chr14:64675400-64695200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr14:64675400-64696200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr14:64675600-64691800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr14:64676200-64690000	Weak transcription	Stomach Mucosa	stomach
40	chr14:64676600-64689000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr14:64676600-64696200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr14:64676800-64691200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr14:64676800-64698800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr14:64677000-64698600	Weak transcription	NHLF	lung
45	chr14:64677000-64698800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr14:64677000-64699400	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr14:64677200-64690000	Weak transcription	A549	lung
48	chr14:64677200-64691800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr14:64677200-64698600	Weak transcription	NHDF-Ad	bronchial
50	chr14:64677400-64697800	Strong transcription	Fetal Stomach	stomach

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