Variant report

Variant	rs1152591
Chromosome Location	chr14:64680848-64680849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64679549..64681782-chr14:64683797..64685712,2	K562	blood:

Variant related genes	Relation type
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10148269	0.95[CHB][hapmap];0.87[YRI][hapmap]
rs10151658	0.83[MKK][hapmap];0.88[YRI][hapmap]
rs1152577	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1152578	0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1152579	0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1152582	0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1152586	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1152588	0.95[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1152589	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]
rs1152590	0.89[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs1152592	0.89[CHB][hapmap];0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs1152593	0.86[ASN][1000 genomes]
rs1152594	0.89[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs1152595	0.84[ASN][1000 genomes]
rs1152601	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs1255984	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1255986	0.84[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1255988	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1255990	0.89[CHB][hapmap]
rs1256030	0.90[CHB][hapmap]
rs1256036	0.95[CHB][hapmap];0.88[YRI][hapmap]
rs1256037	0.94[CHB][hapmap];0.88[YRI][hapmap]
rs1256038	0.95[CHB][hapmap];0.88[YRI][hapmap]
rs1256043	0.89[CHB][hapmap];0.88[YRI][hapmap]
rs1256044	0.90[CHB][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap]
rs1256045	0.90[CHB][hapmap];0.87[YRI][hapmap]
rs1256048	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1256056	0.95[CHB][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1256059	0.95[CHB][hapmap];0.82[GIH][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1256065	0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1262242	0.89[CHB][hapmap]
rs1266927	0.87[AFR][1000 genomes]
rs1269056	0.90[CHB][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap]
rs1760988	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2738413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7229	0.95[CHB][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes]
rs872227	0.89[CHB][hapmap]
rs915057	0.95[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs928554	0.95[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs944046	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs944047	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs960069	0.94[CHB][hapmap];0.88[YRI][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

Variant related diseases (count:1)

Disease	PMID	Source
Atrial fibrillation	22544366	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1152591	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1152591	SYNE2	cis	multi-tissue	Pritchard
rs1152591	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1152591	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1152591	ESR2	cis	Skin Sun Exposed Lower leg	GTEx
rs1152591	MTHFD1	cis	cerebellum	SCAN
rs1152591	MTHFD1	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64660800-64682600	Weak transcription	Hela-S3	cervix
2	chr14:64664000-64699600	Weak transcription	Small Intestine	intestine
3	chr14:64664200-64698600	Weak transcription	HMEC	breast
4	chr14:64665400-64700200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr14:64666200-64686000	Weak transcription	Brain Hippocampus Middle	brain
6	chr14:64666800-64699400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr14:64667400-64690200	Weak transcription	HepG2	liver
8	chr14:64667600-64686200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr14:64669200-64682000	Weak transcription	Fetal Brain Male	brain
10	chr14:64672800-64696600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr14:64674600-64696000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr14:64674600-64696200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr14:64674600-64696400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr14:64674600-64699800	Strong transcription	Liver	Liver
15	chr14:64674800-64683400	Strong transcription	Fetal Brain Female	brain
16	chr14:64674800-64683800	Strong transcription	Adipose Nuclei	Adipose
17	chr14:64674800-64684400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr14:64674800-64686800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr14:64674800-64689000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr14:64674800-64689000	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr14:64674800-64692400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr14:64674800-64692600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr14:64674800-64692800	Strong transcription	Primary T cells from cord blood	blood
24	chr14:64674800-64695800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr14:64674800-64696000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr14:64674800-64696000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr14:64674800-64696000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr14:64674800-64696200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr14:64674800-64696200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr14:64674800-64696200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr14:64674800-64696400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr14:64674800-64696400	Strong transcription	Dnd41	blood
33	chr14:64674800-64696800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr14:64674800-64697600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr14:64674800-64698400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr14:64674800-64699000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr14:64674800-64700000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr14:64674800-64700600	Strong transcription	Fetal Intestine Large	intestine
39	chr14:64675000-64685000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr14:64675000-64689000	Strong transcription	Aorta	Aorta
41	chr14:64675000-64696400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr14:64675000-64696400	Strong transcription	Brain Germinal Matrix	brain
43	chr14:64675200-64683400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr14:64675200-64696400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr14:64675400-64687600	Strong transcription	Brain Anterior Caudate	brain
46	chr14:64675400-64689200	Strong transcription	Rectal Smooth Muscle	rectum
47	chr14:64675400-64695200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr14:64675400-64696200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr14:64675600-64691800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr14:64676200-64682400	Weak transcription	Colon Smooth Muscle	Colon

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