Variant report

Variant	rs12505484
Chromosome Location	chr4:88275699-88275700
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	chr4:88275546..88276371-chr4:88386699..88387600,2	MCF-7	breast:
2	chr4:88275401..88278298-chr4:88313681..88315567,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11097131	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097147	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721653	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11726577	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734330	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737402	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11930147	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11930151	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939903	0.82[AFR][1000 genomes]
rs11946007	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55764266	0.88[EUR][1000 genomes]
rs55879514	0.82[AFR][1000 genomes]
rs55895035	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55932175	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56113853	0.80[AFR][1000 genomes]
rs56141705	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56258452	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56284919	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56385009	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56390566	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56788263	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs58360495	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59157345	0.88[AFR][1000 genomes]
rs60597105	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60955120	0.82[AFR][1000 genomes]
rs61646372	0.82[AFR][1000 genomes]
rs62305726	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305728	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305729	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs62305730	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305731	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305732	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305753	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62319084	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72652029	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73839192	0.88[AFR][1000 genomes]
rs73841141	0.89[AFR][1000 genomes]
rs73841142	0.89[AFR][1000 genomes]
rs73841144	0.89[AFR][1000 genomes]
rs73841145	0.89[AFR][1000 genomes]
rs7664717	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7665549	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7671557	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674658	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690170	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv4412	chr4:88237813-88283368	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer 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	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12505484	HSD17B13	cis	Nerve Tibial	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:88255000-88292400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:88255200-88285600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:88255200-88293800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:88255800-88278200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:88256200-88292800	Weak transcription	Gastric	stomach
7	chr4:88256200-88310600	Weak transcription	Right Ventricle	heart
8	chr4:88257000-88291000	Weak transcription	HUVEC	blood vessel
9	chr4:88257800-88311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:88258000-88278000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:88258000-88285400	Weak transcription	Small Intestine	intestine
12	chr4:88259200-88277200	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:88259200-88283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:88261000-88280000	Weak transcription	Left Ventricle	heart
15	chr4:88261000-88283200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:88261200-88285000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr4:88262200-88280200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:88263000-88277000	Weak transcription	Lung	lung
19	chr4:88263000-88277000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:88263000-88278000	Weak transcription	Stomach Mucosa	stomach
21	chr4:88263000-88280000	Weak transcription	Pancreas	Pancrea
22	chr4:88263200-88281600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr4:88264000-88277000	Weak transcription	HSMM	muscle
24	chr4:88264200-88285600	Weak transcription	Spleen	Spleen
25	chr4:88264400-88279800	Weak transcription	Hela-S3	cervix
26	chr4:88266200-88285000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:88266400-88278200	Weak transcription	Brain Angular Gyrus	brain
28	chr4:88266400-88292200	Weak transcription	Fetal Brain Male	brain
29	chr4:88266600-88278000	Weak transcription	Thymus	Thymus
30	chr4:88266600-88288200	Weak transcription	Brain Germinal Matrix	brain
31	chr4:88267200-88281400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr4:88267400-88278000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr4:88267400-88278000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:88267400-88290600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:88267400-88308000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:88267600-88277000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr4:88267600-88292400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:88267800-88277800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:88267800-88306000	Weak transcription	Fetal Brain Female	brain
40	chr4:88268000-88277000	Weak transcription	Primary T cells from cord blood	blood
41	chr4:88268000-88280000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:88268000-88292200	Weak transcription	Ovary	ovary
43	chr4:88271200-88298000	Weak transcription	HSMMtube	muscle
44	chr4:88273000-88292200	Weak transcription	Brain Substantia Nigra	brain
45	chr4:88273400-88298800	Weak transcription	Fetal Heart	heart
46	chr4:88273800-88284000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:88274200-88278000	Strong transcription	Liver	Liver
48	chr4:88274200-88279000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr4:88274200-88281000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr4:88274200-88288200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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