Variant report

Variant	rs4396926
Chromosome Location	chr3:195987723-195987724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:195986241..195988788-chr3:196013204..196014924,2	MCF-7	breast:
2	chr3:195986524..195988790-chr3:196013840..196016157,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161217	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11914521	0.81[ASN][1000 genomes]
rs11929532	0.81[ASN][1000 genomes]
rs12629949	0.99[ASN][1000 genomes]
rs12632779	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12633502	0.83[ASN][1000 genomes]
rs12634304	0.98[ASN][1000 genomes]
rs12634587	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12635925	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12637288	0.98[ASN][1000 genomes]
rs12637379	0.81[ASN][1000 genomes]
rs1357289	0.81[ASN][1000 genomes]
rs1357290	0.81[AMR][1000 genomes]
rs1948690	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2047551	0.97[ASN][1000 genomes]
rs2088666	1.00[ASN][1000 genomes]
rs2293160	0.81[ASN][1000 genomes]
rs3772107	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3772108	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3772109	0.97[ASN][1000 genomes]
rs4916421	1.00[ASN][1000 genomes]
rs4916424	0.81[ASN][1000 genomes]
rs4916425	0.81[ASN][1000 genomes]
rs4916456	1.00[ASN][1000 genomes]
rs4916477	0.81[ASN][1000 genomes]
rs4916485	0.83[ASN][1000 genomes]
rs55878253	0.81[ASN][1000 genomes]
rs55996879	0.85[ASN][1000 genomes]
rs56240083	0.81[ASN][1000 genomes]
rs56370923	0.81[ASN][1000 genomes]
rs56701784	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57987393	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58297632	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58845625	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59289255	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59352354	1.00[ASN][1000 genomes]
rs60167422	0.83[AMR][1000 genomes]
rs60216585	0.81[ASN][1000 genomes]
rs60336404	0.81[ASN][1000 genomes]
rs61442465	0.90[ASN][1000 genomes]
rs61588443	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66487782	1.00[ASN][1000 genomes]
rs66780758	1.00[ASN][1000 genomes]
rs66805306	1.00[ASN][1000 genomes]
rs66927787	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66942309	0.83[ASN][1000 genomes]
rs67199839	0.83[AMR][1000 genomes]
rs67204670	0.83[ASN][1000 genomes]
rs67317524	0.81[ASN][1000 genomes]
rs67349960	1.00[ASN][1000 genomes]
rs67600689	0.81[ASN][1000 genomes]
rs6762272	0.81[ASN][1000 genomes]
rs6766480	0.84[ASN][1000 genomes]
rs67784045	1.00[ASN][1000 genomes]
rs6778879	0.81[ASN][1000 genomes]
rs68056570	1.00[ASN][1000 genomes]
rs6809764	0.84[ASN][1000 genomes]
rs72611187	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72611188	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72611189	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72611190	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73212160	0.81[ASN][1000 genomes]
rs73212178	0.83[ASN][1000 genomes]
rs7617236	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7635355	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7636149	1.00[ASN][1000 genomes]
rs7640304	1.00[ASN][1000 genomes]
rs870339	0.81[ASN][1000 genomes]
rs9714038	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4396926	TCTEX1D2	cis	Adipose Subcutaneous	GTEx
rs4396926	TCTEX1D2	cis	Esophagus Muscularis	GTEx
rs4396926	TM4SF19-AS1	cis	Nerve Tibial	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	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
6	chr3:195973400-195997200	Weak transcription	Small Intestine	intestine
7	chr3:195974400-195988800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:195974400-195999800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:195974600-195987800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:195974600-195999800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:195974800-195999600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:195974800-195999600	Weak transcription	Pancreas	Pancrea
13	chr3:195974800-196005000	Weak transcription	Stomach Mucosa	stomach
14	chr3:195975000-195988800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:195975000-195988800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:195975000-195988800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:195975000-195990800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:195975000-195994000	Weak transcription	Right Ventricle	heart
19	chr3:195975000-195995000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:195975000-195997200	Weak transcription	Esophagus	oesophagus
21	chr3:195975000-195999600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:195975200-195987800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:195975200-195987800	Weak transcription	HSMMtube	muscle
24	chr3:195975200-195990200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:195975200-195990800	Weak transcription	NHLF	lung
26	chr3:195975200-195991200	Weak transcription	Thymus	Thymus
27	chr3:195975200-195992800	Weak transcription	Brain Anterior Caudate	brain
28	chr3:195975200-195993400	Weak transcription	Aorta	Aorta
29	chr3:195975200-195994200	Weak transcription	Fetal Kidney	kidney
30	chr3:195975200-195994200	Weak transcription	Gastric	stomach
31	chr3:195975400-195992400	Weak transcription	Lung	lung
32	chr3:195975400-195993400	Weak transcription	Colonic Mucosa	Colon
33	chr3:195976400-195994200	Weak transcription	Spleen	Spleen
34	chr3:195977600-195989000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:195978200-195994800	Weak transcription	Brain Angular Gyrus	brain
36	chr3:195978400-195994200	Weak transcription	Brain Substantia Nigra	brain
37	chr3:195978800-195994200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:195979000-195993400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:195979000-195995000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:195980200-195988200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:195981200-195988400	Strong transcription	Fetal Stomach	stomach
42	chr3:195981200-195995200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:195981400-195988200	Strong transcription	Osteobl	bone
44	chr3:195981400-195994600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:195981400-195997800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr3:195982200-195994200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:195982400-195987800	Weak transcription	Fetal Lung	lung
48	chr3:195982400-195997600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:195982600-195989600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:195982800-195995000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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