Variant report

Variant	rs3856466
Chromosome Location	chr2:10916770-10916771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:10916714-10917295	HepG2	liver:	n/a	n/a
2	CTCF	chr2:10916760-10916910	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:10916448-10917070	K562	blood:	n/a	n/a
4	POLR2A	chr2:10916655-10916984	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr2:10916599-10917854	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:10916307-10919284	K562	blood:	n/a	n/a
7	POLR2A	chr2:10915153-10919303	K562	blood:	n/a	n/a
8	POLR2A	chr2:10916734-10916960	A549	lung:	n/a	n/a
9	FOSL2	chr2:10916758-10917688	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:10916350-10919110	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr2:10916667-10917081	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:10916527-10918208	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr2:10916744-10916969	HCT-116	colon:	n/a	n/a
14	POLR2A	chr2:10916568-10916864	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10911679..10916866-chr2:10918103..10925152,7	K562	blood:

Variant related genes	Relation type
ATP6V1C2	TF binding region
ENSG00000143882	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1198844	0.92[EUR][1000 genomes]
rs1198845	0.92[EUR][1000 genomes]
rs1198846	0.92[EUR][1000 genomes]
rs12463454	0.85[ASN][1000 genomes]
rs12464402	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12464513	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12468989	0.92[EUR][1000 genomes]
rs12471725	0.85[ASN][1000 genomes]
rs12471762	0.85[ASN][1000 genomes]
rs12472302	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12475790	0.85[ASN][1000 genomes]
rs12477285	0.83[EUR][1000 genomes]
rs17365181	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17365209	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17365216	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17455708	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17456162	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1817747	0.82[ASN][1000 genomes]
rs2046793	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306922	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856465	0.85[ASN][1000 genomes]
rs55648622	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55675740	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55906240	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55975412	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56093996	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56140102	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56143168	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56147885	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56195743	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56260452	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56264212	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56268818	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66538971	0.91[EUR][1000 genomes]
rs72777379	0.93[EUR][1000 genomes]
rs72777381	0.93[EUR][1000 genomes]
rs72777384	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72777388	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72777393	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72779425	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72779433	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72779445	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10905600-10918000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr2:10906200-10918200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:10906200-10918400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:10908000-10918200	Weak transcription	Pancreas	Pancrea
5	chr2:10908000-10918400	Weak transcription	Aorta	Aorta
6	chr2:10908600-10924400	Weak transcription	Psoas Muscle	Psoas
7	chr2:10908800-10917400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:10908800-10918200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:10910800-10917200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:10911400-10917600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:10912200-10918200	Weak transcription	Primary B cells from cord blood	blood
12	chr2:10912800-10917600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:10913200-10917200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:10913200-10917800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:10913200-10918200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:10913200-10920200	Weak transcription	NH-A	brain
17	chr2:10913400-10917200	Weak transcription	Thymus	Thymus
18	chr2:10913400-10920200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:10913600-10917200	Weak transcription	NHLF	lung
20	chr2:10913600-10918400	Weak transcription	HSMM	muscle
21	chr2:10913600-10919800	Weak transcription	Osteobl	bone
22	chr2:10913800-10917200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:10913800-10917200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:10914200-10917200	Enhancers	Esophagus	oesophagus
25	chr2:10914200-10920000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:10914400-10917200	Weak transcription	Adipose Nuclei	Adipose
27	chr2:10914400-10918000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:10914600-10917400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:10914600-10918400	Weak transcription	HepG2	liver
30	chr2:10914600-10920200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr2:10914600-10922400	Weak transcription	Fetal Kidney	kidney
32	chr2:10914600-10931600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr2:10914800-10917200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:10914800-10917400	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:10914800-10918600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:10915000-10917400	Weak transcription	Liver	Liver
37	chr2:10915000-10917800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:10915000-10918200	Weak transcription	A549	lung
39	chr2:10915000-10920000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr2:10915000-10920000	Weak transcription	Brain Angular Gyrus	brain
41	chr2:10915000-10921600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:10915200-10917600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:10915200-10918000	Weak transcription	Colonic Mucosa	Colon
44	chr2:10915200-10920200	Weak transcription	HSMMtube	muscle
45	chr2:10915200-10923000	Weak transcription	Fetal Brain Male	brain
46	chr2:10915400-10917000	Weak transcription	Primary T cells from cord blood	blood
47	chr2:10915400-10917000	Weak transcription	GM12878-XiMat	blood
48	chr2:10915400-10917200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr2:10915400-10917200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:10915400-10917200	Weak transcription	Fetal Thymus	thymus

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