Variant report

Variant	rs1262242
Chromosome Location	chr14:64653869-64653870
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10148269	0.84[CHB][hapmap]
rs10162323	0.88[CEU][hapmap]
rs1152578	0.83[CHB][hapmap]
rs1152579	0.84[CHB][hapmap]
rs1152582	0.84[CHB][hapmap]
rs1152588	0.84[CHB][hapmap]
rs1152589	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs1152590	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap]
rs1152591	0.89[CHB][hapmap]
rs1152592	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1152594	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap]
rs1152601	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12435376	0.88[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap]
rs1255984	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1255986	0.94[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs1255988	0.90[ASN][1000 genomes]
rs1255990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255991	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255992	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256036	0.84[CHB][hapmap]
rs1256037	0.83[CHB][hapmap]
rs1256038	0.84[CHB][hapmap]
rs1256048	0.84[CHB][hapmap]
rs1256056	0.84[CHB][hapmap]
rs1256059	0.84[CHB][hapmap]
rs1256065	0.84[CHB][hapmap]
rs1266927	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1272715	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1953234	0.83[EUR][1000 genomes]
rs2027094	0.90[CEU][hapmap]
rs2256191	0.82[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2738413	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs2781379	0.92[CEU][hapmap];0.81[YRI][hapmap]
rs2987983	0.80[MEX][hapmap]
rs6573547	0.85[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap]
rs6573548	0.88[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap]
rs7148072	0.88[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap]
rs7229	0.84[CHB][hapmap]
rs872227	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs915057	0.84[CHB][hapmap]
rs928554	0.84[CHB][hapmap]
rs960069	0.83[CHB][hapmap]
rs968257	0.84[CEU][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1262242	SYNE2	cis	multi-tissue	Pritchard
rs1262242	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1262242	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1262242	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1262242	MTHFD1	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64600600-64667400	Weak transcription	Stomach Mucosa	stomach
2	chr14:64625000-64658000	Weak transcription	HUVEC	blood vessel
3	chr14:64627200-64660400	Weak transcription	Fetal Heart	heart
4	chr14:64636400-64658400	Weak transcription	HMEC	breast
5	chr14:64636800-64662600	Weak transcription	Psoas Muscle	Psoas
6	chr14:64637400-64656800	Weak transcription	Hela-S3	cervix
7	chr14:64637400-64663600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:64637600-64655200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr14:64639000-64655000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr14:64639200-64658000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr14:64640000-64663400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr14:64640200-64658000	Weak transcription	NHEK	skin
13	chr14:64642800-64654600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr14:64644600-64658800	Weak transcription	NHLF	lung
15	chr14:64645200-64661000	Weak transcription	Primary B cells from cord blood	blood
16	chr14:64645400-64655400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr14:64645800-64661400	Weak transcription	Small Intestine	intestine
18	chr14:64645800-64663600	Weak transcription	Colonic Mucosa	Colon
19	chr14:64646200-64656200	Weak transcription	Fetal Thymus	thymus
20	chr14:64647000-64655400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:64648000-64654200	Weak transcription	Brain Substantia Nigra	brain
22	chr14:64649000-64654800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr14:64650400-64660000	Strong transcription	Aorta	Aorta
24	chr14:64650400-64660000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr14:64650400-64660200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr14:64650400-64660600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr14:64650600-64655600	Weak transcription	Brain Germinal Matrix	brain
28	chr14:64650800-64658200	Strong transcription	Placenta	Placenta
29	chr14:64650800-64659800	Strong transcription	Left Ventricle	heart
30	chr14:64650800-64661400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr14:64650800-64661600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr14:64650800-64663200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr14:64650800-64671800	Strong transcription	Liver	Liver
34	chr14:64651000-64660400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr14:64651200-64655200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr14:64651200-64655200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr14:64651400-64655400	Weak transcription	Spleen	Spleen
38	chr14:64651400-64659400	Weak transcription	Right Ventricle	heart
39	chr14:64651600-64654400	Weak transcription	Primary T cells from cord blood	blood
40	chr14:64651600-64657400	Strong transcription	GM12878-XiMat	blood
41	chr14:64651600-64662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr14:64651800-64656400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr14:64651800-64661000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr14:64652000-64654400	Weak transcription	Fetal Lung	lung
45	chr14:64652000-64655000	Weak transcription	Adipose Nuclei	Adipose
46	chr14:64652000-64655600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr14:64652000-64658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr14:64652000-64661400	Weak transcription	Fetal Kidney	kidney
49	chr14:64652000-64662800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr14:64652600-64654800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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