Variant report

Variant	rs3890165
Chromosome Location	chr12:120702919-120702920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120684404..120691478-chr12:120697984..120705218,14	MCF-7	breast:
2	chr12:120686832..120689716-chr12:120699360..120703521,4	K562	blood:
3	chr12:120699116..120708865-chr12:120725013..120732311,37	K562	blood:
4	chr12:120663104..120670865-chr12:120700603..120705016,22	K562	blood:
5	chr12:120634894..120637114-chr12:120700788..120703136,2	K562	blood:
6	chr12:120697928..120706288-chr12:120725352..120732223,30	K562	blood:
7	chr12:120553785..120557408-chr12:120702135..120705915,4	K562	blood:
8	chr12:120690051..120707499-chr12:120720410..120732530,91	MCF-7	breast:
9	chr12:120634142..120641127-chr12:120698850..120705439,14	K562	blood:
10	chr12:120683364..120686301-chr12:120702145..120704591,2	K562	blood:
11	chr12:120687678..120692479-chr12:120701581..120703521,4	K562	blood:
12	chr12:120629843..120633670-chr12:120702168..120705891,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000089154	Chromatin interaction
ENSG00000240925	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000089159	Chromatin interaction
ENSG00000255857	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10849739	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11065061	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11065064	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1151824	0.98[EUR][1000 genomes]
rs1151825	0.98[EUR][1000 genomes]
rs1151827	0.98[EUR][1000 genomes]
rs1151830	0.94[EUR][1000 genomes]
rs1151832	0.98[EUR][1000 genomes]
rs1151837	0.98[EUR][1000 genomes]
rs1182860	0.98[EUR][1000 genomes]
rs11831552	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1183781	0.98[EUR][1000 genomes]
rs12164847	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12305146	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12308431	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12321884	0.84[AMR][1000 genomes]
rs12581983	0.86[AMR][1000 genomes]
rs1634814	0.98[EUR][1000 genomes]
rs1634815	0.98[EUR][1000 genomes]
rs2006194	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238156	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238157	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239208	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2283364	0.84[AMR][1000 genomes]
rs2283365	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2524391	0.98[EUR][1000 genomes]
rs3759397	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3888587	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3888588	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3956833	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4767886	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61198412	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7300273	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs739809	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7953949	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7966099	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
2	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases
3	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
4	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
5	nsv560435	chr12:120695141-120769657	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	433 gene(s)	inside rSNPs	diseases
6	nsv899556	chr12:120695141-120779931	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	433 gene(s)	inside rSNPs	diseases
7	nsv560436	chr12:120697470-120705828	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120699600-120703000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:120699600-120703000	Flanking Active TSS	Brain Hippocampus Middle	brain
3	chr12:120699600-120703000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr12:120699600-120703200	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr12:120699600-120703600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:120699800-120703000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr12:120699800-120703000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr12:120699800-120703000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr12:120699800-120703200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr12:120700000-120703000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
11	chr12:120700000-120703000	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr12:120700000-120703000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr12:120700000-120703000	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr12:120700200-120703000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr12:120700200-120703000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:120700200-120703400	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr12:120700200-120703800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr12:120700400-120703000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
19	chr12:120700400-120703000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:120700600-120703200	Flanking Active TSS	Placenta	Placenta
21	chr12:120700600-120703600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:120700800-120703000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:120700800-120703000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr12:120701000-120703800	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr12:120701200-120703000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:120701400-120703000	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr12:120701400-120703600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr12:120701400-120703600	Active TSS	Aorta	Aorta
29	chr12:120701400-120703600	Active TSS	Placenta Amnion	Placenta Amnion
30	chr12:120701400-120703800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:120701600-120703200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:120701600-120703200	Flanking Active TSS	Right Ventricle	heart
33	chr12:120701600-120703600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:120701600-120703800	Active TSS	Fetal Kidney	kidney
35	chr12:120701600-120703800	Active TSS	NHDF-Ad	bronchial
36	chr12:120701800-120703000	Flanking Active TSS	Liver	Liver
37	chr12:120701800-120703200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:120701800-120703200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr12:120701800-120703200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr12:120701800-120703200	Flanking Active TSS	Colonic Mucosa	Colon
41	chr12:120701800-120703200	Flanking Active TSS	Pancreas	Pancrea
42	chr12:120701800-120703400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:120701800-120703600	Active TSS	HSMMtube	muscle
44	chr12:120702000-120703000	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr12:120702000-120703000	Flanking Active TSS	Spleen	Spleen
46	chr12:120702000-120703200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:120702000-120703600	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr12:120702000-120703600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:120702200-120703000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:120702200-120703200	Flanking Active TSS	Dnd41	blood

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