Variant report

Variant	rs2270419
Chromosome Location	chr14:77751925-77751926
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	REST	chr14:77751705-77751933	K562	blood:	n/a	n/a
2	REST	chr14:77751664-77751937	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:77741494..77746628-chr14:77751488..77756217,6	MCF-7	breast:
2	chr14:77750609..77752387-chr14:77785082..77786796,2	MCF-7	breast:
3	chr14:77751328..77755884-chr14:77785355..77788655,4	MCF-7	breast:

Variant related genes	Relation type
POMT2	TF binding region
ENSG00000009830	Chromatin interaction
ENSG00000100577	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10132619	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs1017186	0.86[CHB][hapmap]
rs1046428	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs11847091	1.00[CHD][hapmap]
rs11850308	0.86[CHB][hapmap]
rs11850771	0.86[CHB][hapmap]
rs12894594	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894718	0.86[CHB][hapmap]
rs1468951	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs17105724	1.00[CHD][hapmap]
rs1861888	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2111700	0.86[CHB][hapmap]
rs2160838	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs2363640	0.88[CHB][hapmap];0.86[GIH][hapmap];0.86[ASN][1000 genomes]
rs2364155	0.86[CHB][hapmap]
rs3209079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs369202	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3759731	0.86[CHB][hapmap]
rs3815625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383064	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4141640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451925	0.93[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4899649	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4903566	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap]
rs7146741	0.82[EUR][1000 genomes]
rs8014716	0.86[ASN][1000 genomes]
rs9671248	0.86[CHB][hapmap]
rs972725	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv1361	chr14:77707417-77753024	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv902104	chr14:77720741-77756321	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2270419	ACOT4	cis	parietal	SCAN
rs2270419	FAM75C1	trans	lymphoblastoid	seeQTL
rs2270419	POMT2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77739600-77775600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr14:77740200-77766800	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr14:77740200-77769800	Weak transcription	Small Intestine	intestine
4	chr14:77740400-77766000	Weak transcription	Stomach Mucosa	stomach
5	chr14:77740800-77758000	Strong transcription	Fetal Stomach	stomach
6	chr14:77740800-77766200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr14:77741000-77767400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr14:77741400-77753600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr14:77741800-77752000	Weak transcription	Psoas Muscle	Psoas
10	chr14:77741800-77755400	Strong transcription	Fetal Muscle Leg	muscle
11	chr14:77741800-77757200	Strong transcription	Liver	Liver
12	chr14:77741800-77758600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr14:77741800-77773600	Weak transcription	GM12878-XiMat	blood
14	chr14:77742000-77756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr14:77742000-77757400	Weak transcription	Right Atrium	heart
16	chr14:77742000-77766600	Strong transcription	Placenta	Placenta
17	chr14:77742200-77755000	Strong transcription	Lung	lung
18	chr14:77742200-77757600	Strong transcription	Ovary	ovary
19	chr14:77742200-77767600	Strong transcription	Stomach Smooth Muscle	stomach
20	chr14:77742400-77752200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr14:77742400-77753000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr14:77742400-77755000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr14:77742400-77755200	Strong transcription	Brain Cingulate Gyrus	brain
24	chr14:77742400-77766400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr14:77742400-77766400	Strong transcription	Adipose Nuclei	Adipose
26	chr14:77742400-77780200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr14:77742600-77752200	Strong transcription	Pancreas	Pancrea
28	chr14:77742600-77753200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr14:77742600-77753600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr14:77742600-77755000	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr14:77742600-77755200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr14:77742600-77755200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr14:77742600-77756600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr14:77742600-77757400	Strong transcription	Brain Substantia Nigra	brain
35	chr14:77742600-77759400	Strong transcription	Brain Anterior Caudate	brain
36	chr14:77742600-77759600	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr14:77742600-77766600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr14:77742800-77754400	Strong transcription	Aorta	Aorta
39	chr14:77742800-77755400	Strong transcription	Brain Hippocampus Middle	brain
40	chr14:77742800-77755400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr14:77742800-77757200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr14:77743200-77760400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr14:77743400-77754400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr14:77743400-77754800	Strong transcription	A549	lung
45	chr14:77743400-77757600	Strong transcription	Left Ventricle	heart
46	chr14:77744000-77771400	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr14:77744400-77752800	Strong transcription	Brain Angular Gyrus	brain
48	chr14:77744400-77760200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr14:77745400-77755200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr14:77746200-77755200	Strong transcription	NHEK	skin

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