Variant report

Variant	rs1554957
Chromosome Location	chr14:78007871-78007872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11159272	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11627851	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11629330	0.86[ASW][hapmap]
rs12101160	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12883503	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12885954	0.92[ASN][1000 genomes]
rs12897996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17751727	0.86[ASW][hapmap]
rs1967637	0.96[ASN][1000 genomes]
rs2091914	0.83[ASN][1000 genomes]
rs2284229	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34174438	0.92[ASN][1000 genomes]
rs35487377	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35647237	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4903590	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4903591	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4903593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4903595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4903599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4903602	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8018783	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8020216	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[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	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1554957	GSTZ1	cis	parietal	SCAN
rs1554957	SPTLC2	Cis_1M	lymphoblastoid	RTeQTL
rs1554957	C14orf174	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77970200-78047200	Weak transcription	Fetal Heart	heart
2	chr14:77972000-78018000	Weak transcription	Hela-S3	cervix
3	chr14:77978000-78013400	Weak transcription	NHDF-Ad	bronchial
4	chr14:77978600-78014600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr14:77978800-78042200	Weak transcription	Fetal Brain Male	brain
6	chr14:77979000-78009400	Weak transcription	Stomach Mucosa	stomach
7	chr14:77979000-78013800	Weak transcription	Pancreas	Pancrea
8	chr14:77985200-78008800	Weak transcription	Gastric	stomach
9	chr14:77985200-78014800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr14:77985400-78015000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr14:77986200-78013800	Weak transcription	Esophagus	oesophagus
12	chr14:77986800-78008600	Weak transcription	Brain Germinal Matrix	brain
13	chr14:77987400-78009200	Weak transcription	Aorta	Aorta
14	chr14:77987400-78021000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr14:77987600-78010200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr14:77987600-78010600	Weak transcription	Left Ventricle	heart
17	chr14:77987800-78008800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr14:77987800-78008800	Weak transcription	Fetal Thymus	thymus
19	chr14:77987800-78013400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr14:77987800-78013600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr14:77987800-78013800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr14:77987800-78014600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr14:77987800-78014600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr14:77987800-78014800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr14:77987800-78015000	Weak transcription	Thymus	Thymus
26	chr14:77987800-78015600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr14:77988000-78008200	Weak transcription	Fetal Muscle Leg	muscle
29	chr14:77988000-78008800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr14:77988000-78008800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr14:77988000-78009000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr14:77988000-78010200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr14:77988000-78010600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr14:77988000-78010800	Weak transcription	Dnd41	blood
35	chr14:77988000-78013800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr14:77988000-78013800	Weak transcription	Colonic Mucosa	Colon
37	chr14:77988000-78014600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr14:77988000-78014800	Weak transcription	HMEC	breast
39	chr14:77988000-78015200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr14:77988000-78015600	Weak transcription	Right Ventricle	heart
41	chr14:77988400-78013000	Weak transcription	Small Intestine	intestine
42	chr14:77988400-78013800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr14:77988400-78029400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr14:77988600-78013400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr14:77989600-78008800	Weak transcription	NH-A	brain
46	chr14:77989800-78009000	Weak transcription	Psoas Muscle	Psoas
47	chr14:77989800-78009600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr14:77990000-78010600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr14:77990400-78010800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr14:77990600-78008200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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