Variant report

Variant	rs1152601
Chromosome Location	chr14:64667337-64667338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:64667324-64667528	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64660849..64663610-chr14:64666392..64667974,2	MCF-7	breast:
2	chr14:64657113..64659774-chr14:64664998..64667785,2	MCF-7	breast:

Variant related genes	Relation type
SYNE2	TF binding region
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10148269	0.83[CHB][hapmap]
rs10162323	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1152578	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1152579	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1152582	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1152588	0.83[CHB][hapmap]
rs1152589	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1152590	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1152591	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs1152592	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1152593	0.81[AMR][1000 genomes]
rs1152594	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1152595	0.88[AFR][1000 genomes]
rs12435376	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs1255984	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1255986	0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs1255988	0.88[ASN][1000 genomes]
rs1255990	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1255991	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1255992	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1256036	0.83[CHB][hapmap]
rs1256037	0.83[CHB][hapmap]
rs1256038	0.83[CHB][hapmap]
rs1256048	0.83[CHB][hapmap]
rs1256056	0.83[CHB][hapmap]
rs1256059	0.83[CHB][hapmap]
rs1256065	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1262242	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]
rs1266927	0.92[ASN][1000 genomes]
rs1272715	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2027094	0.90[CEU][hapmap]
rs2256191	0.86[CEU][hapmap]
rs2738413	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs2781379	0.88[CEU][hapmap]
rs6573547	0.87[CEU][hapmap]
rs6573548	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs7148072	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7229	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs872227	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs915057	0.83[CHB][hapmap]
rs928554	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs960069	0.83[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1152601	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1152601	SYNE2	cis	multi-tissue	Pritchard
rs1152601	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1152601	ESR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64600600-64667400	Weak transcription	Stomach Mucosa	stomach
2	chr14:64650800-64671800	Strong transcription	Liver	Liver
3	chr14:64660800-64682600	Weak transcription	Hela-S3	cervix
4	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr14:64661800-64675400	Weak transcription	NHEK	skin
7	chr14:64661800-64675600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr14:64662400-64675200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr14:64662800-64667400	Weak transcription	Lung	lung
10	chr14:64662800-64674800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr14:64663200-64667400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr14:64663800-64668600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr14:64664000-64667400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr14:64664000-64668000	Weak transcription	Spleen	Spleen
15	chr14:64664000-64699600	Weak transcription	Small Intestine	intestine
16	chr14:64664200-64668600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr14:64664200-64675000	Weak transcription	Aorta	Aorta
18	chr14:64664200-64675000	Weak transcription	Colonic Mucosa	Colon
19	chr14:64664200-64675400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr14:64664200-64676200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr14:64664200-64698600	Weak transcription	HMEC	breast
22	chr14:64664400-64667600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr14:64664400-64668000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr14:64664400-64668600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr14:64664400-64669200	Enhancers	Fetal Lung	lung
26	chr14:64664400-64672800	Weak transcription	Fetal Kidney	kidney
27	chr14:64664400-64675800	Weak transcription	NHLF	lung
28	chr14:64664800-64669400	Enhancers	Ovary	ovary
29	chr14:64664800-64672200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr14:64665000-64667400	Weak transcription	Primary B cells from cord blood	blood
31	chr14:64665000-64671000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr14:64665000-64672400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr14:64665000-64673800	Enhancers	Thymus	Thymus
34	chr14:64665000-64674800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr14:64665000-64675600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr14:64665200-64668400	Enhancers	Right Ventricle	heart
37	chr14:64665200-64670800	Enhancers	Pancreas	Pancrea
38	chr14:64665200-64672000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr14:64665200-64676600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr14:64665400-64667400	Weak transcription	Fetal Brain Female	brain
41	chr14:64665400-64667600	Enhancers	Psoas Muscle	Psoas
42	chr14:64665400-64667800	Weak transcription	Fetal Brain Male	brain
43	chr14:64665400-64668000	Enhancers	Adipose Nuclei	Adipose
44	chr14:64665400-64674800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr14:64665400-64675400	Weak transcription	Brain Anterior Caudate	brain
46	chr14:64665400-64700200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr14:64665600-64667400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr14:64665600-64667600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr14:64665800-64668000	Enhancers	Gastric	stomach
50	chr14:64666000-64675200	Weak transcription	Brain Cingulate Gyrus	brain

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