Variant report

Variant	rs2238199
Chromosome Location	chr14:72799003-72799004
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72785270..72787957-chr14:72798250..72801124,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10138180	0.88[CEU][hapmap]
rs12894979	0.80[TSI][hapmap]
rs1520331	0.92[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1520332	0.92[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs1996662	0.90[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2090737	0.96[CEU][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2239224	0.88[CEU][hapmap]
rs2239231	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2239233	0.86[EUR][1000 genomes]
rs2239248	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2239249	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2283390	0.92[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs2332831	0.88[CEU][hapmap]
rs2529466	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2681721	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2681728	0.92[CEU][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2681742	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2681754	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs2681761	0.91[CEU][hapmap]
rs4903003	0.80[TSI][hapmap]
rs847326	0.90[CEU][hapmap]
rs847327	0.91[CEU][hapmap]
rs847333	0.88[CEU][hapmap]
rs847347	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs847351	0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs847352	0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs847353	0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs847354	0.85[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs847356	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs847357	0.86[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	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2238199	C14orf115	cis	cerebellum	SCAN
rs2238199	TMED10	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72796400-72801000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr14:72796600-72799800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr14:72796600-72801400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr14:72797400-72801000	Enhancers	Fetal Stomach	stomach
5	chr14:72797400-72801400	Enhancers	Brain Germinal Matrix	brain
6	chr14:72797600-72799200	Enhancers	Stomach Smooth Muscle	stomach
7	chr14:72797600-72799400	Enhancers	Left Ventricle	heart
8	chr14:72797600-72800000	Enhancers	Fetal Muscle Leg	muscle
9	chr14:72797600-72804800	Enhancers	Fetal Lung	lung
10	chr14:72797800-72799200	Enhancers	Colon Smooth Muscle	Colon
11	chr14:72797800-72799400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr14:72798200-72799400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr14:72798200-72799400	Enhancers	Primary hematopoietic stem cells	blood
14	chr14:72798200-72799400	Enhancers	Lung	lung
15	chr14:72798200-72800800	Enhancers	Fetal Brain Female	brain
16	chr14:72798200-72801200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr14:72798200-72801400	Enhancers	Fetal Brain Male	brain
18	chr14:72798400-72799200	Enhancers	Brain Anterior Caudate	brain
19	chr14:72798400-72799200	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr14:72798400-72799200	Enhancers	Spleen	Spleen
21	chr14:72798800-72799200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr14:72798800-72799200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr14:72798800-72799600	Enhancers	Brain Hippocampus Middle	brain
24	chr14:72798800-72800600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr14:72798800-72800600	Enhancers	Ovary	ovary
26	chr14:72798800-72800800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr14:72798800-72802200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr14:72799000-72799800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr14:72799000-72799800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr14:72799000-72801000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr14:72799000-72801800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr14:72799000-72802200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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