Variant report

Variant	rs59289255
Chromosome Location	chr3:195981299-195981300
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:195971582..195973149-chr3:195978489..195981811,3	MCF-7	breast:
2	chr3:195980853..195983804-chr3:196012474..196014154,2	MCF-7	breast:
3	chr3:195980367..195983637-chr3:196012923..196015535,4	MCF-7	breast:
4	chr3:195979094..195980840-chr3:195981274..195983857,2	K562	blood:

Variant related genes	Relation type
ENSG00000161217	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12629949	0.95[ASN][1000 genomes]
rs12632779	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12633502	0.83[ASN][1000 genomes]
rs12634304	0.94[ASN][1000 genomes]
rs12634587	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12635925	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12637288	0.94[ASN][1000 genomes]
rs1948690	0.96[ASN][1000 genomes]
rs2047551	0.93[ASN][1000 genomes]
rs2088666	0.96[ASN][1000 genomes]
rs3772107	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3772108	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3772109	0.93[ASN][1000 genomes]
rs4396926	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4916421	0.96[ASN][1000 genomes]
rs4916456	0.96[ASN][1000 genomes]
rs4916485	0.83[ASN][1000 genomes]
rs55996879	0.86[ASN][1000 genomes]
rs56701784	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57987393	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58297632	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58845625	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59352354	0.96[ASN][1000 genomes]
rs60167422	0.81[AMR][1000 genomes]
rs61442465	0.87[ASN][1000 genomes]
rs61588443	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66487782	0.96[ASN][1000 genomes]
rs66780758	0.96[ASN][1000 genomes]
rs66805306	0.96[ASN][1000 genomes]
rs66927787	0.96[ASN][1000 genomes]
rs66942309	0.83[ASN][1000 genomes]
rs67199839	0.81[AMR][1000 genomes]
rs67204670	0.83[ASN][1000 genomes]
rs67349960	0.96[ASN][1000 genomes]
rs6766480	0.81[ASN][1000 genomes]
rs67784045	0.96[ASN][1000 genomes]
rs68056570	0.96[ASN][1000 genomes]
rs6809764	0.81[ASN][1000 genomes]
rs72611187	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72611188	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72611189	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72611190	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73212178	0.83[ASN][1000 genomes]
rs7617236	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7635355	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7636149	0.96[ASN][1000 genomes]
rs7640304	0.96[ASN][1000 genomes]
rs870339	0.81[ASN][1000 genomes]
rs9714038	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
10	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
11	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
12	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
14	nsv878178	chr3:195929268-195998451	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
16	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
17	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
18	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
19	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
20	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
21	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59289255	TM4SF19-AS1	cis	Nerve Tibial	GTEx
rs59289255	TCTEX1D2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195965200-195994200	Weak transcription	A549	lung
2	chr3:195965800-196012400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:195967200-195988600	Strong transcription	Fetal Intestine Small	intestine
4	chr3:195968800-195993400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:195969600-195982400	Weak transcription	Fetal Heart	heart
6	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
7	chr3:195973400-195997200	Weak transcription	Small Intestine	intestine
8	chr3:195974400-195988800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:195974400-195999800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:195974600-195981600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:195974600-195981800	Weak transcription	Brain Germinal Matrix	brain
12	chr3:195974600-195981800	Weak transcription	Psoas Muscle	Psoas
13	chr3:195974600-195981800	Weak transcription	NHDF-Ad	bronchial
14	chr3:195974600-195982400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:195974600-195983600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:195974600-195987800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:195974600-195999800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:195974800-195999600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:195974800-195999600	Weak transcription	Pancreas	Pancrea
20	chr3:195974800-196005000	Weak transcription	Stomach Mucosa	stomach
21	chr3:195975000-195981400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:195975000-195981400	Weak transcription	Fetal Thymus	thymus
23	chr3:195975000-195981600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:195975000-195981600	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:195975000-195981800	Weak transcription	HepG2	liver
26	chr3:195975000-195982200	Weak transcription	Hela-S3	cervix
27	chr3:195975000-195982400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:195975000-195983400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:195975000-195983600	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:195975000-195984200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:195975000-195984400	Weak transcription	Fetal Brain Female	brain
32	chr3:195975000-195988800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:195975000-195988800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:195975000-195988800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:195975000-195990800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:195975000-195994000	Weak transcription	Right Ventricle	heart
37	chr3:195975000-195995000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr3:195975000-195997200	Weak transcription	Esophagus	oesophagus
39	chr3:195975000-195999600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:195975200-195981400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:195975200-195981400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:195975200-195981400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:195975200-195981400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:195975200-195981400	Weak transcription	Liver	Liver
45	chr3:195975200-195981400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:195975200-195981400	Weak transcription	Placenta	Placenta
47	chr3:195975200-195981400	Weak transcription	Left Ventricle	heart
48	chr3:195975200-195981400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr3:195975200-195981400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:195975200-195981400	Weak transcription	Osteobl	bone

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