Variant report

Variant	rs2268982
Chromosome Location	chr14:69412804-69412805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:69402982..69422523-chr14:69436263..69448017,46	MCF-7	breast:
2	chr14:69260918..69263431-chr14:69412114..69414632,2	MCF-7	breast:
3	chr14:69402918..69410408-chr14:69410942..69415819,17	MCF-7	breast:
4	chr14:69403117..69416483-chr14:69441657..69449888,50	MCF-7	breast:
5	chr14:69390453..69396616-chr14:69408232..69413432,8	MCF-7	breast:
6	chr14:69391007..69391868-chr14:69412625..69413278,3	MCF-7	breast:
7	chr14:69391007..69391868-chr14:69412642..69413278,3	MCF-7	breast:
8	chr14:69412106..69413788-chr14:69432458..69434178,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000072110	Chromatin interaction
ENSG00000185650	Chromatin interaction
ENSG00000259062	Chromatin interaction
ENSG00000258531	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1009145	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.96[ASN][1000 genomes]
rs10141794	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12588423	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2268975	0.88[CHB][hapmap]
rs2268976	0.88[CHB][hapmap];0.84[AMR][1000 genomes]
rs2268977	0.88[CHB][hapmap]
rs2268978	0.82[ASW][hapmap]
rs2268980	0.86[AFR][1000 genomes]
rs2268983	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.91[ASN][1000 genomes]
rs2268985	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.96[ASN][1000 genomes]
rs2268986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2300876	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2300878	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28574858	0.96[ASN][1000 genomes]
rs3742897	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs3784137	0.84[CHB][hapmap]
rs3784139	0.82[ASW][hapmap]
rs3784140	0.89[CHB][hapmap]
rs4902672	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs72733532	0.86[ASN][1000 genomes]
rs8010464	0.83[CHB][hapmap]
rs8010912	0.87[CHB][hapmap]
rs8011150	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	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv564964	chr14:69392264-69423164	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv456333	chr14:69392445-69415962	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv564965	chr14:69392445-69415962	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2268982	SYNE2	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69387400-69420400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr14:69394200-69422200	Weak transcription	Dnd41	blood
3	chr14:69397800-69415200	Enhancers	Esophagus	oesophagus
4	chr14:69399000-69423200	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr14:69400200-69416400	Enhancers	Pancreas	Pancrea
6	chr14:69400400-69417000	Enhancers	Fetal Muscle Leg	muscle
7	chr14:69400800-69420400	Enhancers	Fetal Lung	lung
8	chr14:69402000-69426200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr14:69402200-69425200	Enhancers	Right Atrium	heart
10	chr14:69402400-69414400	Enhancers	Adipose Nuclei	Adipose
11	chr14:69402400-69416400	Enhancers	Left Ventricle	heart
12	chr14:69402400-69423600	Enhancers	Fetal Heart	heart
13	chr14:69402400-69427000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr14:69402600-69416600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr14:69403600-69420400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr14:69404200-69417000	Enhancers	Right Ventricle	heart
17	chr14:69405000-69415400	Weak transcription	Psoas Muscle	Psoas
18	chr14:69405400-69413600	Enhancers	Liver	Liver
19	chr14:69406000-69413000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr14:69406400-69417800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr14:69406800-69414400	Genic enhancers	Fetal Intestine Small	intestine
22	chr14:69407000-69414600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr14:69407000-69414600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr14:69407000-69419600	Weak transcription	Fetal Brain Male	brain
25	chr14:69407200-69414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:69407400-69416400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr14:69408000-69413800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr14:69408400-69416400	Genic enhancers	Fetal Stomach	stomach
29	chr14:69408400-69416600	Enhancers	Brain Anterior Caudate	brain
30	chr14:69408400-69416600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr14:69408600-69414600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr14:69409000-69414000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr14:69409200-69414200	Enhancers	Colonic Mucosa	Colon
34	chr14:69409200-69414200	Genic enhancers	NH-A	brain
35	chr14:69409400-69414800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
36	chr14:69409400-69416400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr14:69409600-69414200	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr14:69409600-69414400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr14:69409600-69414600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr14:69409800-69413200	Genic enhancers	NHEK	skin
41	chr14:69409800-69434400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr14:69410000-69414200	Genic enhancers	Osteobl	bone
43	chr14:69410000-69414400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr14:69410000-69416200	Enhancers	Fetal Intestine Large	intestine
45	chr14:69410200-69416400	Enhancers	Lung	lung
46	chr14:69410200-69420200	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr14:69410400-69416600	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr14:69410600-69413800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr14:69410600-69413800	Enhancers	Thymus	Thymus
50	chr14:69410600-69416600	Enhancers	Fetal Thymus	thymus

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