Variant report

Variant	rs928554
Chromosome Location	chr14:64694195-64694196
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10148269	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10151658	0.88[MKK][hapmap];0.88[YRI][hapmap]
rs1152577	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1152578	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1152579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1152582	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1152586	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1152588	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]
rs1152589	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]
rs1152590	0.84[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1152591	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]
rs1152592	0.84[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1152593	0.86[ASN][1000 genomes]
rs1152594	0.84[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1152595	0.81[ASN][1000 genomes]
rs1152601	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1255984	0.89[CHB][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.88[YRI][hapmap]
rs1255986	0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs1255988	0.86[AFR][1000 genomes]
rs1255990	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs1256030	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1256031	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs1256033	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs1256036	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1256037	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1256038	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1256039	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1256041	0.87[AMR][1000 genomes]
rs1256042	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1256043	0.86[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1256044	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1256045	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1256046	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1256048	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1256056	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1256059	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1256065	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1262242	0.84[CHB][hapmap]
rs1266927	0.84[AFR][1000 genomes]
rs1269056	0.84[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1271573	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1760988	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2738413	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3020445	0.84[CEU][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap]
rs3783736	0.83[GIH][hapmap]
rs7229	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs872227	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs915057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs944046	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs944047	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs960069	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs928554	MTHFD1	cis	parietal	SCAN
rs928554	C15orf59	trans	parietal	SCAN
rs928554	ESR2	cis	Skin Sun Exposed Lower leg	GTEx
rs928554	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs928554	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs928554	SYNE2	cis	multi-tissue	Pritchard
rs928554	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 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	chr14:64672800-64696600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr14:64674600-64696000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr14:64674600-64696200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr14:64674600-64696400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr14:64674600-64699800	Strong transcription	Liver	Liver
10	chr14:64674800-64695800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr14:64674800-64696000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr14:64674800-64696000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr14:64674800-64696000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr14:64674800-64696200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:64674800-64696200	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr14:64674800-64696200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr14:64674800-64696400	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr14:64674800-64696400	Strong transcription	Dnd41	blood
19	chr14:64674800-64696800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr14:64674800-64697600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr14:64674800-64698400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr14:64674800-64699000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:64674800-64700000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr14:64674800-64700600	Strong transcription	Fetal Intestine Large	intestine
25	chr14:64675000-64696400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr14:64675000-64696400	Strong transcription	Brain Germinal Matrix	brain
27	chr14:64675200-64696400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr14:64675400-64695200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr14:64675400-64696200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr14:64676600-64696200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr14:64676800-64698800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr14:64677000-64698600	Weak transcription	NHLF	lung
33	chr14:64677000-64698800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr14:64677000-64699400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr14:64677200-64698600	Weak transcription	NHDF-Ad	bronchial
36	chr14:64677400-64697800	Strong transcription	Fetal Stomach	stomach
37	chr14:64677600-64698200	Strong transcription	Colonic Mucosa	Colon
38	chr14:64679800-64698200	Weak transcription	HUVEC	blood vessel
39	chr14:64679800-64698800	Weak transcription	NH-A	brain
40	chr14:64680600-64694800	Strong transcription	Fetal Intestine Small	intestine
41	chr14:64681600-64698800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr14:64684400-64696800	Strong transcription	Adipose Nuclei	Adipose
43	chr14:64684400-64699600	Strong transcription	Placenta	Placenta
44	chr14:64684600-64696600	Strong transcription	Fetal Brain Female	brain
45	chr14:64684600-64696800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr14:64685200-64696000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr14:64685400-64696000	Strong transcription	Fetal Lung	lung
48	chr14:64685800-64696200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr14:64686000-64694400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr14:64686000-64696200	Strong transcription	Lung	lung

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