Variant report

Variant	rs12633827
Chromosome Location	chr3:196026208-196026209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196025894..196029484-chr3:196038924..196041076,3	K562	blood:
2	chr3:196019342..196021385-chr3:196024989..196026503,2	K562	blood:
3	chr3:196013519..196016880-chr3:196025587..196027490,3	K562	blood:
4	chr3:196013519..196016421-chr3:196024534..196027087,2	K562	blood:

Variant related genes	Relation type
ENSG00000161217	Chromatin interaction
ENSG00000213123	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12632779	0.88[ASN][1000 genomes]
rs12633454	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12634350	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12634587	0.88[ASN][1000 genomes]
rs12635925	0.88[ASN][1000 genomes]
rs1357290	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772107	0.88[ASN][1000 genomes]
rs3772108	0.85[ASN][1000 genomes]
rs4916484	0.82[ASN][1000 genomes]
rs55996879	0.87[EUR][1000 genomes]
rs56701784	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57987393	0.84[ASN][1000 genomes]
rs58297632	0.81[EUR][1000 genomes]
rs58568267	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58845625	0.88[ASN][1000 genomes]
rs59708858	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60167422	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61254593	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61588443	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66935510	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67199839	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72611187	0.88[ASN][1000 genomes]
rs72611189	0.86[ASN][1000 genomes]
rs72611190	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73212156	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7617236	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7635355	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12633827	TM4SF19	cis	Muscle Skeletal	GTEx
rs12633827	TCTEX1D2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196015200-196038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:196015200-196044400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:196015400-196028800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:196015400-196030200	Weak transcription	NHDF-Ad	bronchial
5	chr3:196015400-196033000	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:196015400-196043800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:196015400-196043800	Weak transcription	Fetal Kidney	kidney
8	chr3:196015400-196043800	Weak transcription	Fetal Lung	lung
9	chr3:196015400-196044400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:196015400-196044400	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:196015400-196044400	Weak transcription	Lung	lung
12	chr3:196015600-196026400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:196015600-196026800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:196015600-196026800	Weak transcription	Ovary	ovary
15	chr3:196015600-196027800	Weak transcription	Brain Anterior Caudate	brain
16	chr3:196015600-196028200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:196015600-196028800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:196015600-196034200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:196015600-196034400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:196015600-196034800	Weak transcription	HSMMtube	muscle
21	chr3:196015600-196036200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:196015600-196041400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:196015600-196043600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:196015600-196043600	Weak transcription	Fetal Brain Male	brain
25	chr3:196015600-196043800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:196015600-196043800	Weak transcription	Brain Angular Gyrus	brain
27	chr3:196015600-196044200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:196015600-196044200	Weak transcription	Adipose Nuclei	Adipose
29	chr3:196015600-196044400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:196015800-196026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:196015800-196026800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:196015800-196026800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:196015800-196026800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:196015800-196028000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:196015800-196028800	Weak transcription	Osteobl	bone
36	chr3:196015800-196029000	Weak transcription	NHEK	skin
37	chr3:196015800-196038800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:196015800-196042800	Weak transcription	HMEC	breast
39	chr3:196015800-196043000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:196015800-196043400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:196015800-196043600	Weak transcription	A549	lung
42	chr3:196015800-196043800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:196015800-196043800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:196015800-196043800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:196015800-196043800	Weak transcription	HSMM	muscle
46	chr3:196015800-196044200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:196015800-196044400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:196016000-196026800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:196016000-196043600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr3:196016000-196043600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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