Variant report

Variant	rs4902308
Chromosome Location	chr14:39499158-39499159
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39457540..39460115-chr14:39498272..39500421,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10133797	0.86[CHB][hapmap];0.93[GIH][hapmap];0.82[MKK][hapmap]
rs10134230	0.81[AMR][1000 genomes]
rs10134654	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10136536	0.86[CHB][hapmap];0.93[GIH][hapmap];0.82[MKK][hapmap]
rs10137988	0.90[CEU][hapmap];0.94[CHD][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10140341	0.92[ASN][1000 genomes]
rs10140949	0.81[AMR][1000 genomes]
rs10141255	0.81[AMR][1000 genomes]
rs10141471	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10151683	0.84[CHB][hapmap]
rs1061583	0.86[CHB][hapmap];0.93[GIH][hapmap];0.90[MKK][hapmap]
rs11157041	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12050319	0.81[AMR][1000 genomes]
rs12147991	0.86[CHB][hapmap];0.93[GIH][hapmap];0.90[MKK][hapmap]
rs12164875	0.84[CEU][hapmap]
rs12434847	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12437031	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12437346	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12878139	0.81[AMR][1000 genomes]
rs12878789	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12879229	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12882868	0.81[AMR][1000 genomes]
rs12883061	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12885242	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12890771	0.90[CEU][hapmap];0.94[CHD][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1555257	0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.96[ASN][1000 genomes]
rs17108728	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17108846	0.86[CHB][hapmap];0.93[GIH][hapmap];0.90[MKK][hapmap]
rs1957064	0.81[AMR][1000 genomes]
rs2415524	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2737721	0.86[CHB][hapmap];0.93[GIH][hapmap]
rs2737729	0.86[CHB][hapmap]
rs2753606	0.86[CHB][hapmap]
rs28367031	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28502115	0.94[ASN][1000 genomes]
rs2869	0.86[CHB][hapmap];0.93[GIH][hapmap]
rs28699217	0.89[ASN][1000 genomes]
rs28810420	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34642409	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34676226	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34985331	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35224434	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35287240	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35423721	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35712728	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35807641	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35992529	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36161173	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742354	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.94[ASN][1000 genomes]
rs3742355	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759545	0.86[CHB][hapmap];0.93[GIH][hapmap];0.82[MKK][hapmap]
rs4143954	0.86[CHB][hapmap];0.89[GIH][hapmap]
rs4902259	0.85[CEU][hapmap];0.91[CHD][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4902418	0.86[CHB][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap]
rs4902431	0.86[CHB][hapmap];0.93[GIH][hapmap];0.82[MKK][hapmap]
rs4902448	0.86[CHB][hapmap];0.87[GIH][hapmap]
rs6571893	0.94[ASN][1000 genomes]
rs71407775	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7147194	0.86[CHB][hapmap];0.93[GIH][hapmap]
rs7150092	0.81[AMR][1000 genomes]
rs7151246	0.81[AMR][1000 genomes]
rs7152746	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9743575	0.81[AMR][1000 genomes]
rs975521	0.93[AMR][1000 genomes];0.86[EUR][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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv564417	chr14:39452317-39535560	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4902308	TRAPPC6B	cis	multi-tissue	Pritchard
rs4902308	TRAPPC6B	cis	cerebellum	SCAN
rs4902308	FIBP	trans	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39482800-39499200	Weak transcription	Right Ventricle	heart
2	chr14:39487000-39499400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr14:39487200-39508600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr14:39491400-39499200	Weak transcription	NHEK	skin
5	chr14:39493400-39505800	Weak transcription	Psoas Muscle	Psoas
6	chr14:39495400-39505000	Weak transcription	Small Intestine	intestine
7	chr14:39495400-39505800	Weak transcription	Fetal Kidney	kidney
8	chr14:39495400-39518200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr14:39495600-39499200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr14:39495600-39499200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr14:39495600-39509800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:39495800-39516000	Weak transcription	Stomach Mucosa	stomach
13	chr14:39496000-39514800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr14:39496000-39520400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr14:39496400-39499600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr14:39496600-39499600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:39496600-39500000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr14:39496600-39507800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr14:39497200-39500000	Strong transcription	HUVEC	blood vessel
20	chr14:39497400-39499400	Weak transcription	Brain Angular Gyrus	brain
21	chr14:39497400-39503200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr14:39497400-39506000	Weak transcription	Fetal Heart	heart
23	chr14:39497400-39518000	Strong transcription	HSMM	muscle
24	chr14:39497400-39519200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr14:39497600-39499200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr14:39497600-39499200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr14:39497600-39499200	Weak transcription	Fetal Thymus	thymus
28	chr14:39497600-39499200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr14:39497600-39499400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr14:39497600-39499800	Strong transcription	A549	lung
31	chr14:39497600-39501000	Weak transcription	Hela-S3	cervix
32	chr14:39497600-39507600	Weak transcription	Brain Germinal Matrix	brain
33	chr14:39497800-39499600	Weak transcription	Primary B cells from cord blood	blood
34	chr14:39497800-39500200	Strong transcription	Colonic Mucosa	Colon
35	chr14:39497800-39500600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr14:39497800-39500600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr14:39497800-39502400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr14:39497800-39505800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr14:39497800-39520400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr14:39497800-39521200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr14:39498000-39499600	Weak transcription	Colon Smooth Muscle	Colon
42	chr14:39498000-39499600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr14:39498000-39500200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr14:39498000-39500200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr14:39498000-39501000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr14:39498000-39502000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr14:39498000-39502200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr14:39498000-39505800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr14:39498000-39510000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr14:39498000-39518400	Strong transcription	Osteobl	bone

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