Variant report

Variant	rs1152589
Chromosome Location	chr14:64683926-64683927
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:64662559..64666637-chr14:64681435..64684914,4	MCF-7	breast:
2	chr14:64657632..64659971-chr14:64682618..64684745,2	MCF-7	breast:
3	chr14:64682929..64685902-chr14:64969733..64972022,2	MCF-7	breast:
4	chr14:64679549..64681782-chr14:64683797..64685712,2	K562	blood:

Variant related genes	Relation type
ENSG00000054654	Chromatin interaction
ENSG00000089775	Chromatin interaction
ENSG00000126804	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10148269	0.89[CHB][hapmap]
rs1152577	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1152578	0.89[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1152579	0.89[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1152582	0.89[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1152586	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1152588	0.89[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1152590	0.94[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1152591	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1152592	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1152593	0.87[ASN][1000 genomes]
rs1152594	0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1152595	0.82[ASN][1000 genomes]
rs1152601	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1255984	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1255986	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1255988	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1255990	0.94[CHB][hapmap]
rs1256030	0.85[CHB][hapmap]
rs1256036	0.89[CHB][hapmap]
rs1256037	0.89[CHB][hapmap]
rs1256038	0.89[CHB][hapmap]
rs1256043	0.84[CHB][hapmap]
rs1256044	0.85[CHB][hapmap];0.82[GIH][hapmap]
rs1256045	0.85[CHB][hapmap]
rs1256048	0.89[CHB][hapmap]
rs1256056	0.89[CHB][hapmap];0.84[AMR][1000 genomes]
rs1256059	0.89[CHB][hapmap];0.84[GIH][hapmap];0.84[AMR][1000 genomes]
rs1256065	0.89[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1256112	0.83[MKK][hapmap]
rs1262242	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs1269056	0.85[CHB][hapmap];0.82[GIH][hapmap]
rs1760988	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2738413	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3020445	0.88[MKK][hapmap]
rs7229	0.89[CHB][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs872227	0.94[CHB][hapmap]
rs915057	0.89[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs928554	0.89[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs944046	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs944047	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs960069	0.89[CHB][hapmap]

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
rs1152589	SYNE2	cis	multi-tissue	Pritchard
rs1152589	ESR2	cis	Skin Sun Exposed Lower leg	GTEx

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	chr14:64666200-64686000	Weak transcription	Brain Hippocampus Middle	brain
5	chr14:64666800-64699400	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr14:64667400-64690200	Weak transcription	HepG2	liver
7	chr14:64667600-64686200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr14:64672800-64696600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr14:64674600-64696000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr14:64674600-64696200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr14:64674600-64696400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr14:64674600-64699800	Strong transcription	Liver	Liver
13	chr14:64674800-64684400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:64674800-64686800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr14:64674800-64689000	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr14:64674800-64689000	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr14:64674800-64692400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr14:64674800-64692600	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr14:64674800-64692800	Strong transcription	Primary T cells from cord blood	blood
20	chr14:64674800-64695800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr14:64674800-64696000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr14:64674800-64696000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr14:64674800-64696000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr14:64674800-64696200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr14:64674800-64696200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr14:64674800-64696200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr14:64674800-64696400	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr14:64674800-64696400	Strong transcription	Dnd41	blood
29	chr14:64674800-64696800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr14:64674800-64697600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr14:64674800-64698400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr14:64674800-64699000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:64674800-64700000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr14:64674800-64700600	Strong transcription	Fetal Intestine Large	intestine
35	chr14:64675000-64685000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr14:64675000-64689000	Strong transcription	Aorta	Aorta
37	chr14:64675000-64696400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr14:64675000-64696400	Strong transcription	Brain Germinal Matrix	brain
39	chr14:64675200-64696400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr14:64675400-64687600	Strong transcription	Brain Anterior Caudate	brain
41	chr14:64675400-64689200	Strong transcription	Rectal Smooth Muscle	rectum
42	chr14:64675400-64695200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr14:64675400-64696200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr14:64675600-64691800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr14:64676200-64690000	Weak transcription	Stomach Mucosa	stomach
46	chr14:64676600-64689000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr14:64676600-64696200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr14:64676800-64691200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr14:64676800-64698800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr14:64677000-64687200	Weak transcription	Muscle Satellite Cultured Cells	--

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