Variant report

Variant	rs60167422
Chromosome Location	chr3:196016986-196016987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196013567..196017227-chr3:196043342..196045325,4	MCF-7	breast:
2	chr3:196015046..196017473-chr3:196021246..196023038,2	K562	blood:
3	chr3:196014434..196017243-chr3:196157002..196159307,2	K562	blood:

Variant related genes	Relation type
ENSG00000272741	Chromatin interaction
ENSG00000225822	Chromatin interaction
ENSG00000213123	Chromatin interaction
ENSG00000235897	Chromatin interaction
ENSG00000163960	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12632779	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12633454	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12633827	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12634350	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12634587	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12635925	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1357290	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3772107	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3772108	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4396926	0.83[AMR][1000 genomes]
rs4916484	0.84[ASN][1000 genomes]
rs55996879	0.85[EUR][1000 genomes]
rs56701784	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57987393	0.87[ASN][1000 genomes]
rs58297632	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58568267	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58845625	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59289255	0.81[AMR][1000 genomes]
rs59708858	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61254593	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61588443	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66935510	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67199839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6762272	0.81[AMR][1000 genomes]
rs72611187	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72611188	0.86[AMR][1000 genomes]
rs72611189	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72611190	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73212156	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73212176	0.81[ASN][1000 genomes]
rs7617236	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7635355	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
13	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
14	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
15	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
16	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
17	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
18	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
rs60167422	TM4SF19	cis	Muscle Skeletal	GTEx
rs60167422	TCTEX1D2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:75 , 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	chr3:196015400-196023000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:196015400-196024400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:196015400-196028800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:196015400-196030200	Weak transcription	NHDF-Ad	bronchial
7	chr3:196015400-196033000	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:196015400-196043800	Weak transcription	Brain Substantia Nigra	brain
9	chr3:196015400-196043800	Weak transcription	Fetal Kidney	kidney
10	chr3:196015400-196043800	Weak transcription	Fetal Lung	lung
11	chr3:196015400-196044400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:196015400-196044400	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:196015400-196044400	Weak transcription	Lung	lung
14	chr3:196015600-196020000	Weak transcription	Psoas Muscle	Psoas
15	chr3:196015600-196020200	Weak transcription	Fetal Stomach	stomach
16	chr3:196015600-196020800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:196015600-196021200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:196015600-196021600	Weak transcription	Fetal Intestine Small	intestine
19	chr3:196015600-196026200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:196015600-196026200	Weak transcription	Thymus	Thymus
21	chr3:196015600-196026400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:196015600-196026800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:196015600-196026800	Weak transcription	Ovary	ovary
24	chr3:196015600-196027800	Weak transcription	Brain Anterior Caudate	brain
25	chr3:196015600-196028200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:196015600-196028800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:196015600-196034200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:196015600-196034400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:196015600-196034800	Weak transcription	HSMMtube	muscle
30	chr3:196015600-196036200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:196015600-196041400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:196015600-196043600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:196015600-196043600	Weak transcription	Fetal Brain Male	brain
34	chr3:196015600-196043800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:196015600-196043800	Weak transcription	Brain Angular Gyrus	brain
36	chr3:196015600-196044200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:196015600-196044200	Weak transcription	Adipose Nuclei	Adipose
38	chr3:196015600-196044400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:196015800-196017000	Weak transcription	Hela-S3	cervix
40	chr3:196015800-196017200	Weak transcription	Fetal Intestine Large	intestine
41	chr3:196015800-196017400	Weak transcription	GM12878-XiMat	blood
42	chr3:196015800-196018200	Weak transcription	Fetal Brain Female	brain
43	chr3:196015800-196020800	Weak transcription	Fetal Thymus	thymus
44	chr3:196015800-196021200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:196015800-196021400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:196015800-196021400	Weak transcription	Brain Germinal Matrix	brain
47	chr3:196015800-196024600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:196015800-196024600	Weak transcription	Fetal Muscle Leg	muscle
49	chr3:196015800-196024800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:196015800-196025600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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