Variant report

Variant	rs56240083
Chromosome Location	chr3:196039966-196039967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196037781..196041667-chr3:196043629..196046627,4	MCF-7	breast:
2	chr3:196039550..196042176-chr3:196054293..196056157,2	K562	blood:
3	chr3:196025894..196029484-chr3:196038924..196041076,3	K562	blood:
4	chr3:196038505..196041350-chr3:196041984..196044639,3	K562	blood:
5	chr3:196038442..196040771-chr3:196041248..196043484,3	K562	blood:
6	chr3:196012130..196017200-chr3:196038456..196041932,5	MCF-7	breast:
7	chr3:196038994..196040619-chr3:196228993..196230606,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272741	Chromatin interaction
ENSG00000235897	Chromatin interaction
ENSG00000163961	Chromatin interaction
ENSG00000161217	Chromatin interaction
ENSG00000213123	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11914521	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11929532	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629949	0.80[ASN][1000 genomes]
rs12633502	0.83[ASN][1000 genomes]
rs12637379	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1357289	1.00[ASN][1000 genomes]
rs1948690	0.81[ASN][1000 genomes]
rs2088666	0.81[ASN][1000 genomes]
rs2293160	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4396926	0.81[ASN][1000 genomes]
rs4916421	0.81[ASN][1000 genomes]
rs4916424	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916425	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916456	0.81[ASN][1000 genomes]
rs4916476	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916477	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916479	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4916485	0.83[ASN][1000 genomes]
rs55878253	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55903345	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55996879	0.85[ASN][1000 genomes]
rs56370923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58297632	0.81[ASN][1000 genomes]
rs59352354	0.81[ASN][1000 genomes]
rs60216585	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60336404	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66487782	0.81[ASN][1000 genomes]
rs66780758	0.81[ASN][1000 genomes]
rs66805306	0.81[ASN][1000 genomes]
rs66927787	0.81[ASN][1000 genomes]
rs66942309	0.83[ASN][1000 genomes]
rs67204670	0.83[ASN][1000 genomes]
rs67317524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67349960	0.81[ASN][1000 genomes]
rs67600689	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762272	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766480	0.97[ASN][1000 genomes]
rs6768240	0.81[ASN][1000 genomes]
rs67784045	0.81[ASN][1000 genomes]
rs6778879	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67947474	0.81[ASN][1000 genomes]
rs68056570	0.81[ASN][1000 genomes]
rs6809764	0.97[ASN][1000 genomes]
rs72611188	0.80[ASN][1000 genomes]
rs73212155	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73212160	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73212178	0.83[ASN][1000 genomes]
rs7616433	0.86[ASN][1000 genomes]
rs7636149	0.81[ASN][1000 genomes]
rs7640304	0.81[ASN][1000 genomes]
rs9714038	0.81[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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv1003764	chr3:196028141-196190687	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
19	nsv536895	chr3:196028141-196190687	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
20	nsv4183	chr3:196034067-196079109	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56240083	TCTEX1D2	cis	Skin Sun Exposed Lower leg	GTEx
rs56240083	TCTEX1D2	cis	Adipose Subcutaneous	GTEx
rs56240083	TM4SF19	cis	Muscle Skeletal	GTEx
rs56240083	TCTEX1D2	cis	Artery Tibial	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196015200-196044400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:196015400-196043800	Weak transcription	Brain Substantia Nigra	brain
3	chr3:196015400-196043800	Weak transcription	Fetal Kidney	kidney
4	chr3:196015400-196043800	Weak transcription	Fetal Lung	lung
5	chr3:196015400-196044400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:196015400-196044400	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:196015400-196044400	Weak transcription	Lung	lung
8	chr3:196015600-196041400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:196015600-196043600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:196015600-196043600	Weak transcription	Fetal Brain Male	brain
11	chr3:196015600-196043800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:196015600-196043800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:196015600-196044200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:196015600-196044200	Weak transcription	Adipose Nuclei	Adipose
15	chr3:196015600-196044400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:196015800-196042800	Weak transcription	HMEC	breast
17	chr3:196015800-196043000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:196015800-196043400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:196015800-196043600	Weak transcription	A549	lung
20	chr3:196015800-196043800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:196015800-196043800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:196015800-196043800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:196015800-196043800	Weak transcription	HSMM	muscle
24	chr3:196015800-196044200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:196015800-196044400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:196016000-196043600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:196016000-196043600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:196018600-196044200	Weak transcription	Fetal Intestine Large	intestine
29	chr3:196023200-196044400	Weak transcription	Left Ventricle	heart
30	chr3:196023400-196044400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:196024800-196043600	Weak transcription	GM12878-XiMat	blood
32	chr3:196025200-196044400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:196025600-196043800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:196026400-196044200	Weak transcription	Placenta	Placenta
35	chr3:196027400-196043800	Weak transcription	Thymus	Thymus
36	chr3:196027600-196041600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:196027800-196044200	Weak transcription	Fetal Intestine Small	intestine
38	chr3:196028200-196043800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:196029000-196044200	Weak transcription	Brain Anterior Caudate	brain
40	chr3:196029400-196041000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:196029400-196043600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:196029600-196041000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:196029600-196043600	Weak transcription	Osteobl	bone
44	chr3:196029600-196043800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:196029600-196043800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:196030200-196044200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:196030600-196041600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:196030600-196043600	Weak transcription	NHDF-Ad	bronchial
49	chr3:196030600-196043800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:196031200-196043600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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