Variant report

Variant	rs57125237
Chromosome Location	chr2:10828849-10828850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr2:10828475-10830867	SK-N-SH	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10804991..10808517-chr2:10827670..10830075,3	K562	blood:
2	chr2:10828248..10829978-chr2:10860553..10862190,2	MCF-7	breast:
3	chr2:10828658..10831241-chr2:10859513..10862984,4	MCF-7	breast:
4	chr2:10584788..10589777-chr2:10826863..10830293,6	K562	blood:
5	chr2:10825832..10829197-chr2:10829233..10832096,3	K562	blood:
6	chr2:10828291..10832221-chr2:11269738..11273006,3	MCF-7	breast:

No data

Variant related genes	Relation type
RN7SL832P	TF binding region
ENSG00000145063	Chromatin interaction
ENSG00000243819	Chromatin interaction
ENSG00000115761	Chromatin interaction
ENSG00000143882	Chromatin interaction
ENSG00000257135	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000206633	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs2171771	1.00[AMR][1000 genomes]
rs56702784	1.00[AMR][1000 genomes]
rs56914795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57309175	1.00[AMR][1000 genomes]
rs57382387	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57464659	1.00[AMR][1000 genomes]
rs57597544	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58214362	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58838965	1.00[AMR][1000 genomes]
rs58886768	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59114654	1.00[AMR][1000 genomes]
rs59640725	1.00[AMR][1000 genomes]
rs60016454	1.00[AMR][1000 genomes]
rs60286502	1.00[AMR][1000 genomes]
rs60384217	1.00[AMR][1000 genomes]
rs60489255	1.00[AMR][1000 genomes]
rs61167760	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6749287	1.00[AMR][1000 genomes]
rs73165980	1.00[AMR][1000 genomes]
rs73167824	1.00[AMR][1000 genomes]
rs73167845	1.00[AMR][1000 genomes]
rs73167849	1.00[AMR][1000 genomes]
rs73167864	1.00[AMR][1000 genomes]
rs73167887	1.00[AMR][1000 genomes]
rs73167897	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73167901	1.00[AMR][1000 genomes]
rs73169906	1.00[AMR][1000 genomes]
rs73169907	1.00[AMR][1000 genomes]
rs73169908	1.00[AMR][1000 genomes]
rs73169917	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73169921	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73169922	1.00[AMR][1000 genomes]
rs73169924	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73169925	1.00[AMR][1000 genomes]
rs73169929	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73169933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7587281	1.00[AMR][1000 genomes]
rs7601546	0.82[AFR][1000 genomes]
rs7607468	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv833381	chr2:10723465-10911284	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers 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	21 gene(s)	inside rSNPs	diseases
4	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10800200-10829200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:10805000-10829200	Weak transcription	Aorta	Aorta
3	chr2:10813200-10829200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:10817800-10829400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:10824000-10829000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:10824000-10829200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:10826200-10829000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:10826400-10829400	Enhancers	Spleen	Spleen
9	chr2:10826600-10829000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:10826600-10829000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr2:10826600-10829000	Enhancers	Brain Anterior Caudate	brain
12	chr2:10826600-10829200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:10826800-10829000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr2:10827200-10829000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:10827400-10829000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr2:10827400-10829200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:10827400-10829400	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr2:10827600-10829000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:10827600-10829200	Weak transcription	Ovary	ovary
20	chr2:10827800-10829000	Enhancers	Right Atrium	heart
21	chr2:10828000-10829000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr2:10828000-10829000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:10828000-10829000	Enhancers	Fetal Heart	heart
24	chr2:10828000-10829000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr2:10828000-10829200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr2:10828000-10829200	Enhancers	Esophagus	oesophagus
27	chr2:10828000-10829400	Flanking Active TSS	Dnd41	blood
28	chr2:10828200-10829000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:10828200-10829000	Enhancers	Adipose Nuclei	Adipose
30	chr2:10828200-10829000	Enhancers	Brain Substantia Nigra	brain
31	chr2:10828200-10829000	Enhancers	Fetal Intestine Large	intestine
32	chr2:10828200-10829000	Enhancers	Fetal Lung	lung
33	chr2:10828200-10829000	Enhancers	Fetal Thymus	thymus
34	chr2:10828200-10829200	Enhancers	Primary B cells from peripheral blood	blood
35	chr2:10828200-10829200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr2:10828200-10829200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:10828200-10829200	Enhancers	Small Intestine	intestine
38	chr2:10828200-10829200	Flanking Active TSS	GM12878-XiMat	blood
39	chr2:10828200-10829200	Flanking Active TSS	HepG2	liver
40	chr2:10828200-10829400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:10828200-10829400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:10828200-10829400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:10828200-10829400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:10828200-10829400	Enhancers	Stomach Mucosa	stomach
45	chr2:10828200-10829400	Flanking Active TSS	Hela-S3	cervix
46	chr2:10828200-10829600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:10828200-10829800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:10828200-10829800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:10828200-10829800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr2:10828200-10831200	Active TSS	HUES6 Cell Line	embryonic stem cell

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