Variant report

Variant	rs1255986
Chromosome Location	chr14:64655161-64655162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10148269	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs10151658	0.92[MKK][hapmap];1.00[YRI][hapmap]
rs1152577	0.86[AFR][1000 genomes]
rs1152578	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs1152579	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs1152582	0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes]
rs1152588	0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes]
rs1152589	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]
rs1152590	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs1152591	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]
rs1152592	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1152594	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1152601	0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs1255984	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1255988	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1255990	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1255991	0.92[ASN][1000 genomes]
rs1255992	0.89[ASN][1000 genomes]
rs1256030	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1256036	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs1256037	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs1256038	0.89[CHB][hapmap]
rs1256043	0.84[CHB][hapmap]
rs1256044	0.85[CHB][hapmap];0.80[JPT][hapmap];0.96[MKK][hapmap]
rs1256045	0.85[CHB][hapmap]
rs1256048	0.89[CHB][hapmap];0.80[JPT][hapmap];0.88[YRI][hapmap]
rs1256056	0.89[CHB][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap]
rs1256059	0.89[CHB][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap]
rs1256065	0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs1262242	0.94[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs1266927	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1269056	0.85[CHB][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap]
rs1272715	0.91[ASN][1000 genomes]
rs1760988	0.84[AFR][1000 genomes]
rs2738413	0.84[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7229	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs872227	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs915057	0.89[CHB][hapmap];0.96[MKK][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs928554	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]
rs944046	0.86[AFR][1000 genomes]
rs944047	0.86[AFR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1255986	SYNE2	cis	multi-tissue	Pritchard
rs1255986	ESR2	cis	Skin Sun Exposed Lower leg	GTEx
rs1255986	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1255986	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1255986	MTHFD1	cis	cerebellum	SCAN
rs1255986	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 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	chr14:64639200-64658000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr14:64640000-64663400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr14:64640200-64658000	Weak transcription	NHEK	skin
12	chr14:64644600-64658800	Weak transcription	NHLF	lung
13	chr14:64645200-64661000	Weak transcription	Primary B cells from cord blood	blood
14	chr14:64645400-64655400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr14:64645800-64661400	Weak transcription	Small Intestine	intestine
16	chr14:64645800-64663600	Weak transcription	Colonic Mucosa	Colon
17	chr14:64646200-64656200	Weak transcription	Fetal Thymus	thymus
18	chr14:64647000-64655400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr14:64650400-64660000	Strong transcription	Aorta	Aorta
20	chr14:64650400-64660000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr14:64650400-64660200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr14:64650400-64660600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr14:64650600-64655600	Weak transcription	Brain Germinal Matrix	brain
24	chr14:64650800-64658200	Strong transcription	Placenta	Placenta
25	chr14:64650800-64659800	Strong transcription	Left Ventricle	heart
26	chr14:64650800-64661400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr14:64650800-64661600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr14:64650800-64663200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr14:64650800-64671800	Strong transcription	Liver	Liver
30	chr14:64651000-64660400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr14:64651200-64655200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr14:64651200-64655200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr14:64651400-64655400	Weak transcription	Spleen	Spleen
34	chr14:64651400-64659400	Weak transcription	Right Ventricle	heart
35	chr14:64651600-64657400	Strong transcription	GM12878-XiMat	blood
36	chr14:64651600-64662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr14:64651800-64656400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr14:64651800-64661000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr14:64652000-64655600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr14:64652000-64658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr14:64652000-64661400	Weak transcription	Fetal Kidney	kidney
42	chr14:64652000-64662800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr14:64652600-64655600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr14:64652600-64658000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr14:64652800-64655200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr14:64652800-64658000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr14:64652800-64659000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr14:64652800-64660000	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr14:64652800-64666200	Strong transcription	Dnd41	blood
50	chr14:64653000-64655800	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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