Variant report

Variant	rs10138030
Chromosome Location	chr14:77754547-77754548
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77746501..77748869-chr14:77754519..77757381,3	MCF-7	breast:
2	chr14:77644659..77647131-chr14:77754541..77756569,2	MCF-7	breast:
3	chr14:77741494..77746628-chr14:77751488..77756217,6	MCF-7	breast:
4	chr14:77754082..77755889-chr14:77757491..77759643,2	MCF-7	breast:
5	chr14:77751328..77755884-chr14:77785355..77788655,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100577	Chromatin interaction
ENSG00000009830	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1055592	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs11547793	0.87[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap]
rs11624564	0.95[CHD][hapmap];0.83[JPT][hapmap]
rs12437115	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17105672	0.85[CHD][hapmap]
rs2042045	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs2216089	0.81[CHD][hapmap]
rs2270422	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs2287387	0.98[CHD][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs2287388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2363638	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2363641	0.87[JPT][hapmap]
rs28374503	0.93[ASN][1000 genomes]
rs35149989	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs368855	0.82[MEX][hapmap]
rs3759733	0.87[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs3783986	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[ASN][1000 genomes]
rs3783988	0.94[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs3783989	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3815626	0.87[JPT][hapmap]
rs4899650	0.91[JPT][hapmap]
rs4903567	0.98[CHD][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs4903569	0.80[ASN][1000 genomes]
rs4903570	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6574367	0.87[JPT][hapmap]
rs6636	0.91[CHB][hapmap]
rs6637	0.83[CHB][hapmap]
rs71413458	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7142812	0.87[JPT][hapmap]
rs7158951	0.95[CHD][hapmap];0.83[JPT][hapmap]
rs7159558	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs731346	0.81[CHB][hapmap]
rs8009261	0.95[CHD][hapmap];0.83[JPT][hapmap]
rs8009733	0.95[CHD][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10138030	EIF2B2	cis	cerebellum	SCAN
rs10138030	AHSA1	cis	parietal	SCAN
rs10138030	GSTZ1	cis	lymphoblastoid	seeQTL
rs10138030	POMT2	cis	parietal	SCAN
rs10138030	C14orf156	cis	cerebellum	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	chr14:77741800-77755400	Strong transcription	Fetal Muscle Leg	muscle
9	chr14:77741800-77757200	Strong transcription	Liver	Liver
10	chr14:77741800-77758600	Strong transcription	Fetal Muscle Trunk	muscle
11	chr14:77741800-77773600	Weak transcription	GM12878-XiMat	blood
12	chr14:77742000-77756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr14:77742000-77757400	Weak transcription	Right Atrium	heart
14	chr14:77742000-77766600	Strong transcription	Placenta	Placenta
15	chr14:77742200-77755000	Strong transcription	Lung	lung
16	chr14:77742200-77757600	Strong transcription	Ovary	ovary
17	chr14:77742200-77767600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr14:77742400-77755000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr14:77742400-77755200	Strong transcription	Brain Cingulate Gyrus	brain
20	chr14:77742400-77766400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:77742400-77766400	Strong transcription	Adipose Nuclei	Adipose
22	chr14:77742400-77780200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr14:77742600-77755000	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr14:77742600-77755200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr14:77742600-77755200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr14:77742600-77756600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr14:77742600-77757400	Strong transcription	Brain Substantia Nigra	brain
28	chr14:77742600-77759400	Strong transcription	Brain Anterior Caudate	brain
29	chr14:77742600-77759600	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr14:77742600-77766600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr14:77742800-77755400	Strong transcription	Brain Hippocampus Middle	brain
32	chr14:77742800-77755400	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr14:77742800-77757200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr14:77743200-77760400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr14:77743400-77754800	Strong transcription	A549	lung
36	chr14:77743400-77757600	Strong transcription	Left Ventricle	heart
37	chr14:77744000-77771400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr14:77744400-77760200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr14:77745400-77755200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr14:77746200-77755200	Strong transcription	NHEK	skin
41	chr14:77746600-77767200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr14:77746800-77762200	Weak transcription	Colonic Mucosa	Colon
43	chr14:77747200-77762000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:77747600-77756800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr14:77747800-77755200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr14:77748200-77755200	Strong transcription	Primary T cells from cord blood	blood
47	chr14:77748200-77757400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr14:77748400-77755200	Strong transcription	Spleen	Spleen
49	chr14:77748400-77759200	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr14:77748800-77755200	Strong transcription	Colon Smooth Muscle	Colon

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