Variant report

Variant	rs7143942
Chromosome Location	chr14:39816401-39816402
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10137623	0.87[CHB][hapmap]
rs1056345	0.80[CEU][hapmap]
rs11560068	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12433610	1.00[ASW][hapmap]
rs12891025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12891299	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1570131	0.90[ASW][hapmap];0.88[JPT][hapmap]
rs17109030	0.83[JPT][hapmap]
rs17621388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17692639	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs17694832	0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap]
rs1980609	1.00[ASW][hapmap]
rs2415542	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2415546	0.87[CHB][hapmap];0.86[CHD][hapmap];0.81[MEX][hapmap]
rs34843498	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4531652	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6571912	0.82[ASW][hapmap]
rs7149971	0.81[CEU][hapmap]
rs7153074	0.89[ASW][hapmap]
rs7154632	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs7155164	0.88[JPT][hapmap]
rs8006182	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs8014839	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs8015094	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs8017737	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8020472	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8020596	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7143942	TRAPPC6B	cis	multi-tissue	Pritchard
rs7143942	S100A13	trans	lymphoblastoid	seeQTL
rs7143942	SEC23A	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39756200-39828400	Weak transcription	Brain Germinal Matrix	brain
2	chr14:39756600-39819600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr14:39757400-39843800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:39764600-39818400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr14:39767200-39833800	Weak transcription	Small Intestine	intestine
6	chr14:39770600-39819800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:39770800-39872400	Weak transcription	Colonic Mucosa	Colon
8	chr14:39786600-39828600	Weak transcription	Spleen	Spleen
9	chr14:39786800-39823000	Strong transcription	Liver	Liver
10	chr14:39792800-39841600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr14:39793000-39822200	Weak transcription	Fetal Lung	lung
12	chr14:39794400-39843200	Weak transcription	HUVEC	blood vessel
13	chr14:39796400-39817800	Weak transcription	HSMMtube	muscle
14	chr14:39796400-39828400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:39797000-39837400	Weak transcription	Brain Substantia Nigra	brain
16	chr14:39802000-39835600	Weak transcription	Esophagus	oesophagus
17	chr14:39802000-39841200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr14:39802600-39817000	Weak transcription	NHLF	lung
19	chr14:39802600-39835400	Weak transcription	Psoas Muscle	Psoas
20	chr14:39802800-39822000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr14:39802800-39828400	Weak transcription	Ovary	ovary
22	chr14:39802800-39828400	Weak transcription	Pancreas	Pancrea
23	chr14:39802800-39828600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr14:39802800-39835400	Weak transcription	Gastric	stomach
25	chr14:39802800-39839400	Weak transcription	Aorta	Aorta
26	chr14:39803000-39835400	Weak transcription	Right Ventricle	heart
27	chr14:39803000-39845800	Weak transcription	NHEK	skin
28	chr14:39803200-39818000	Weak transcription	Brain Angular Gyrus	brain
29	chr14:39803200-39824600	Weak transcription	Brain Hippocampus Middle	brain
30	chr14:39803200-39833000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr14:39803200-39838400	Weak transcription	Thymus	Thymus
32	chr14:39803200-39843400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr14:39803200-39845800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr14:39803400-39843800	Weak transcription	HMEC	breast
35	chr14:39807000-39824400	Weak transcription	NH-A	brain
36	chr14:39807400-39836000	Weak transcription	Brain Anterior Caudate	brain
37	chr14:39808400-39819000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr14:39808400-39828400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr14:39808400-39828800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr14:39808400-39841200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr14:39808600-39817400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr14:39808600-39828400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr14:39808600-39828800	Weak transcription	Fetal Heart	heart
44	chr14:39808800-39822200	Weak transcription	A549	lung
45	chr14:39809600-39822400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr14:39809600-39832800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr14:39809800-39828800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr14:39810000-39835200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr14:39811800-39823200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr14:39812200-39818600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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