Variant report

Variant	rs10162323
Chromosome Location	chr14:64668144-64668145
allele	C/T
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	NR2F2	chr14:64667969-64668565	MCF-7	breast:	n/a	n/a
2	ZNF217	chr14:64668134-64668454	MCF-7	breast:	n/a	n/a
3	CTCF	chr14:64668054-64668226	MCF-7	breast:	n/a	n/a
4	CTCF	chr14:64668045-64668232	MCF-7	breast:	n/a	n/a
5	CTCF	chr14:64668044-64668230	MCF-7	breast:	n/a	n/a
6	CTCF	chr14:64668040-64668190	MCF-7	breast:	n/a	n/a
7	CTCF	chr14:64668060-64668219	MCF-7	breast:	n/a	n/a
8	CTCF	chr14:64668060-64668240	MCF-7	breast:	n/a	n/a
9	CTCF	chr14:64668100-64668250	MCF-7	breast:	n/a	n/a
10	HDAC2	chr14:64667968-64668468	MCF-7	breast:	n/a	chr14:64668119-64668138
11	MAX	chr14:64668026-64668484	MCF-7	breast:	n/a	n/a
12	TCF7L2	chr14:64668140-64668393	MCF-7	breast:	n/a	chr14:64668258-64668272 chr14:64668257-64668271

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64667840..64668649-chr14:64760945..64761764,2	MCF-7	breast:
2	chr14:64667402..64671365-chr14:64674791..64677546,5	MCF-7	breast:

Variant related genes	Relation type
SYNE2	TF binding region
ENSG00000140009	Chromatin interaction
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1152590	0.88[CEU][hapmap]
rs1152592	0.84[CEU][hapmap]
rs1152594	0.88[CEU][hapmap]
rs1152601	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12435376	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];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1255990	0.88[CEU][hapmap]
rs1262242	0.88[CEU][hapmap]
rs1953234	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2027094	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2256191	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2776607	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2781379	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2781380	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6573547	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6573548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7148072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7148637	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs872227	0.88[CEU][hapmap]
rs968257	0.85[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10162323	SYNE2	cis	multi-tissue	Pritchard
rs10162323	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs10162323	ESR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64650800-64671800	Strong transcription	Liver	Liver
2	chr14:64660800-64682600	Weak transcription	Hela-S3	cervix
3	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr14:64661800-64675400	Weak transcription	NHEK	skin
6	chr14:64661800-64675600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr14:64662400-64675200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr14:64662800-64674800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr14:64663800-64668600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr14:64664000-64699600	Weak transcription	Small Intestine	intestine
11	chr14:64664200-64668600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr14:64664200-64675000	Weak transcription	Aorta	Aorta
13	chr14:64664200-64675000	Weak transcription	Colonic Mucosa	Colon
14	chr14:64664200-64675400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr14:64664200-64676200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr14:64664200-64698600	Weak transcription	HMEC	breast
17	chr14:64664400-64668600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr14:64664400-64669200	Enhancers	Fetal Lung	lung
19	chr14:64664400-64672800	Weak transcription	Fetal Kidney	kidney
20	chr14:64664400-64675800	Weak transcription	NHLF	lung
21	chr14:64664800-64669400	Enhancers	Ovary	ovary
22	chr14:64664800-64672200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr14:64665000-64671000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr14:64665000-64672400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr14:64665000-64673800	Enhancers	Thymus	Thymus
26	chr14:64665000-64674800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr14:64665000-64675600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr14:64665200-64668400	Enhancers	Right Ventricle	heart
29	chr14:64665200-64670800	Enhancers	Pancreas	Pancrea
30	chr14:64665200-64672000	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr14:64665200-64676600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr14:64665400-64674800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr14:64665400-64675400	Weak transcription	Brain Anterior Caudate	brain
34	chr14:64665400-64700200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr14:64666000-64675200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr14:64666200-64669600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr14:64666200-64674800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr14:64666200-64675400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr14:64666200-64675800	Weak transcription	Brain Angular Gyrus	brain
40	chr14:64666200-64678600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr14:64666200-64686000	Weak transcription	Brain Hippocampus Middle	brain
42	chr14:64666400-64669600	Enhancers	Left Ventricle	heart
43	chr14:64666600-64668200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr14:64666600-64668400	Enhancers	H1 Cell Line	embryonic stem cell
45	chr14:64666600-64668600	Enhancers	Placenta	Placenta
46	chr14:64666600-64669000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr14:64666600-64669000	Enhancers	Fetal Intestine Large	intestine
48	chr14:64666800-64668400	Enhancers	Fetal Heart	heart
49	chr14:64666800-64699400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr14:64667000-64668400	Strong transcription	Primary T cells from cord blood	blood

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