Variant report

Variant	rs67199839
Chromosome Location	chr3:196015772-196015773
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:196013746-196016683	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr3:196015392-196016026	K562	blood:	n/a	n/a
3	POLR2A	chr3:196015510-196016548	PANC-1	pancreas:	n/a	n/a
4	MXI1	chr3:196013686-196016157	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:196015771-196016082	K562	blood:	n/a	n/a
6	POLR2A	chr3:196013997-196015795	K562	blood:	n/a	n/a
7	POLR2A	chr3:196014047-196015860	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr3:196015766-196015903	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr3:196015386-196015783	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr3:196015712-196016202	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:196012776..196015922-chr3:196063347..196066816,3	MCF-7	breast:
2	chr3:196013519..196016421-chr3:196024534..196027087,2	K562	blood:
3	chr3:196012377..196016502-chr3:196041586..196047553,11	K562	blood:
4	chr3:196013567..196017227-chr3:196043342..196045325,4	MCF-7	breast:
5	chr3:196014537..196016415-chr3:196229117..196231929,2	MCF-7	breast:
6	chr3:196014832..196016725-chr3:196229110..196231842,2	K562	blood:
7	chr3:196013815..196016163-chr6:27090213..27092532,2	MCF-7	breast:
8	chr3:196015046..196017473-chr3:196021246..196023038,2	K562	blood:
9	chr3:196014705..196016276-chr3:196018024..196020194,2	K562	blood:
10	chr3:196014550..196016725-chr3:196229110..196232092,4	K562	blood:
11	chr3:196012352..196016755-chr3:196062622..196069148,9	K562	blood:
12	chr3:196012576..196016636-chr3:196061383..196069148,11	K562	blood:
13	chr3:196014592..196016192-chr3:196157861..196160786,2	MCF-7	breast:
14	chr3:196013508..196016403-chr3:196043043..196046288,6	MCF-7	breast:
15	chr3:196013398..196015851-chr3:196068583..196071493,3	MCF-7	breast:
16	chr3:196014434..196017243-chr3:196157002..196159307,2	K562	blood:

No data

Variant related genes	Relation type
PCYT1A	TF binding region
ENSG00000272741	Chromatin interaction
ENSG00000235897	Chromatin interaction
ENSG00000213123	Chromatin interaction
ENSG00000145107	Chromatin interaction
ENSG00000163961	Chromatin interaction
ENSG00000225822	Chromatin interaction
ENSG00000237418	Chromatin interaction
ENSG00000212146	Chromatin interaction
ENSG00000163960	Chromatin interaction
ENSG00000272468	Chromatin interaction
ENSG00000273331	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];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12633454	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[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];0.93[ASN][1000 genomes]
rs12635925	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1357290	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3772107	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3772108	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[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];0.93[ASN][1000 genomes]
rs57987393	0.90[ASN][1000 genomes]
rs58297632	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58568267	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58845625	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59289255	0.81[AMR][1000 genomes]
rs59708858	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60167422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61254593	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61588443	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66935510	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6762272	0.81[AMR][1000 genomes]
rs72611187	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72611188	0.86[AMR][1000 genomes]
rs72611189	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72611190	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[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];0.93[ASN][1000 genomes]
rs7635355	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[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
rs67199839	TCTEX1D2	cis	Adipose Subcutaneous	GTEx
rs67199839	TM4SF19	cis	Muscle Skeletal	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196012600-196015800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:196013200-196015800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:196013400-196015800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr3:196013400-196015800	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr3:196013400-196015800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr3:196013400-196015800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:196013400-196015800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:196013400-196015800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:196013400-196015800	Active TSS	A549	lung
10	chr3:196013400-196015800	Active TSS	HSMM	muscle
11	chr3:196013400-196015800	Active TSS	NHEK	skin
12	chr3:196013400-196016000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:196013600-196015800	Active TSS	H1 Cell Line	embryonic stem cell
14	chr3:196013600-196015800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:196013600-196015800	Active TSS	Fetal Intestine Large	intestine
16	chr3:196013600-196015800	Active TSS	Stomach Smooth Muscle	stomach
17	chr3:196013800-196015800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr3:196014000-196015800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:196014000-196015800	Active TSS	Duodenum Mucosa	Duodenum
20	chr3:196014000-196015800	Active TSS	Hela-S3	cervix
21	chr3:196014000-196015800	Active TSS	Osteobl	bone
22	chr3:196014400-196015800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:196014600-196015800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:196014600-196015800	Active TSS	Brain Germinal Matrix	brain
25	chr3:196014800-196015800	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr3:196015200-196015800	Flanking Active TSS	Dnd41	blood
27	chr3:196015200-196038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:196015200-196044400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:196015400-196015800	Enhancers	Primary B cells from cord blood	blood
30	chr3:196015400-196015800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:196015400-196015800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr3:196015400-196015800	Flanking Active TSS	Fetal Brain Female	brain
33	chr3:196015400-196015800	Enhancers	Fetal Muscle Leg	muscle
34	chr3:196015400-196015800	Enhancers	Placenta	Placenta
35	chr3:196015400-196016000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr3:196015400-196016000	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr3:196015400-196016000	Enhancers	Fetal Heart	heart
38	chr3:196015400-196016200	Enhancers	Primary B cells from peripheral blood	blood
39	chr3:196015400-196016200	Enhancers	Liver	Liver
40	chr3:196015400-196023000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:196015400-196024400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:196015400-196028800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:196015400-196030200	Weak transcription	NHDF-Ad	bronchial
44	chr3:196015400-196033000	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:196015400-196043800	Weak transcription	Brain Substantia Nigra	brain
46	chr3:196015400-196043800	Weak transcription	Fetal Kidney	kidney
47	chr3:196015400-196043800	Weak transcription	Fetal Lung	lung
48	chr3:196015400-196044400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:196015400-196044400	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:196015400-196044400	Weak transcription	Lung	lung

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