Variant report

Variant	rs73212156
Chromosome Location	chr3:196031481-196031482
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196013297..196016411-chr3:196030766..196033177,3	MCF-7	breast:
2	chr3:196029606..196031660-chr3:196035462..196038417,2	K562	blood:
3	chr3:196028161..196030114-chr3:196030783..196032843,2	MCF-7	breast:
4	chr3:196030405..196033243-chr3:196043662..196046190,3	K562	blood:
5	chr3:196030106..196032154-chr3:196042449..196045068,2	K562	blood:

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

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12632779	0.85[ASN][1000 genomes]
rs12633454	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12633827	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12634350	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12634587	0.85[ASN][1000 genomes]
rs12635925	0.85[ASN][1000 genomes]
rs1357290	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3772107	0.85[ASN][1000 genomes]
rs3772108	0.82[ASN][1000 genomes]
rs4916484	0.80[EUR][1000 genomes]
rs55996879	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56701784	0.85[ASN][1000 genomes]
rs57987393	0.82[ASN][1000 genomes]
rs58568267	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58845625	0.85[ASN][1000 genomes]
rs59708858	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60167422	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61254593	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61588443	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66935510	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66942309	0.80[EUR][1000 genomes]
rs67199839	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72611187	0.85[ASN][1000 genomes]
rs72611189	0.83[ASN][1000 genomes]
rs72611190	0.85[ASN][1000 genomes]
rs73212155	0.81[AMR][1000 genomes]
rs73212176	0.80[EUR][1000 genomes]
rs7617236	0.85[ASN][1000 genomes]
rs7635355	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs73212156	TM4SF19	cis	Muscle Skeletal	GTEx
rs73212156	TCTEX1D2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:86 , 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	chr3:196015400-196033000	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:196015400-196043800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:196015400-196043800	Weak transcription	Fetal Kidney	kidney
6	chr3:196015400-196043800	Weak transcription	Fetal Lung	lung
7	chr3:196015400-196044400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:196015400-196044400	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:196015400-196044400	Weak transcription	Lung	lung
10	chr3:196015600-196034200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:196015600-196034400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:196015600-196034800	Weak transcription	HSMMtube	muscle
13	chr3:196015600-196036200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:196015600-196041400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:196015600-196043600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:196015600-196043600	Weak transcription	Fetal Brain Male	brain
17	chr3:196015600-196043800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:196015600-196043800	Weak transcription	Brain Angular Gyrus	brain
19	chr3:196015600-196044200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:196015600-196044200	Weak transcription	Adipose Nuclei	Adipose
21	chr3:196015600-196044400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:196015800-196038800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:196015800-196042800	Weak transcription	HMEC	breast
24	chr3:196015800-196043000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:196015800-196043400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:196015800-196043600	Weak transcription	A549	lung
27	chr3:196015800-196043800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:196015800-196043800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:196015800-196043800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:196015800-196043800	Weak transcription	HSMM	muscle
31	chr3:196015800-196044200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:196015800-196044400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:196016000-196043600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr3:196016000-196043600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:196018600-196044200	Weak transcription	Fetal Intestine Large	intestine
36	chr3:196021200-196033200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:196021400-196033600	Strong transcription	Brain Germinal Matrix	brain
38	chr3:196022000-196032400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:196022600-196033000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:196023200-196044400	Weak transcription	Left Ventricle	heart
41	chr3:196023400-196044400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:196024200-196033600	Weak transcription	NH-A	brain
43	chr3:196024600-196033000	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:196024600-196033200	Strong transcription	Fetal Muscle Leg	muscle
45	chr3:196024800-196033200	Strong transcription	Fetal Stomach	stomach
46	chr3:196024800-196043600	Weak transcription	GM12878-XiMat	blood
47	chr3:196025200-196044400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:196025600-196033200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:196025600-196043800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:196025800-196033200	Weak transcription	HUVEC	blood vessel

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