Variant report

Variant	rs2999286
Chromosome Location	chr10:43928539-43928540
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43901784..43908257-chr10:43928243..43934263,17	MCF-7	breast:
2	chr10:43926891..43929031-chr10:43930226..43934041,5	K562	blood:
3	chr10:43890830..43894030-chr10:43926925..43929713,4	MCF-7	breast:
4	chr10:43901370..43906375-chr10:43928042..43934083,16	MCF-7	breast:
5	chr10:43926632..43929031-chr10:43930226..43934041,5	K562	blood:

Variant related genes	Relation type
ENSG00000243660	Chromatin interaction
ENSG00000169813	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10899797	0.84[ASN][1000 genomes]
rs11238526	0.85[ASN][1000 genomes]
rs1126709	0.86[ASN][1000 genomes]
rs12257917	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2247860	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2247979	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2247981	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2248931	0.81[ASN][1000 genomes]
rs2250444	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2252800	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2255967	0.87[ASN][1000 genomes]
rs2260200	0.83[AFR][1000 genomes]
rs2261636	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2265887	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2265888	0.85[AFR][1000 genomes]
rs2265952	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2265953	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2265954	0.83[AFR][1000 genomes]
rs2492404	0.84[ASN][1000 genomes]
rs2492405	0.85[AFR][1000 genomes]
rs2492407	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2492408	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2492410	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2492411	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2493648	0.83[AFR][1000 genomes]
rs2819032	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2819034	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999287	0.81[AMR][1000 genomes]
rs3000700	0.90[ASN][1000 genomes]
rs4551711	0.81[AFR][1000 genomes]
rs4584528	0.85[AFR][1000 genomes]
rs4948726	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56059584	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61859002	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6421744	0.81[AFR][1000 genomes]
rs7069214	0.83[AFR][1000 genomes]
rs7070029	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7088430	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7905676	0.86[ASN][1000 genomes]
rs9422371	0.81[AFR][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	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	92 gene(s)	inside rSNPs	diseases
2	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv825354	chr10:43883418-43949936	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv825356	chr10:43893080-43946515	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
7	esv3448813	chr10:43919995-43950867	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43916800-43931400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr10:43916800-43931600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr10:43916800-43931600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:43917000-43931600	Weak transcription	Fetal Brain Female	brain
5	chr10:43917200-43930800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:43917200-43930800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr10:43917200-43931600	Weak transcription	Brain Anterior Caudate	brain
8	chr10:43917400-43930400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:43917400-43930800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr10:43917400-43930800	Weak transcription	Brain Hippocampus Middle	brain
11	chr10:43917400-43930800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr10:43917400-43930800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:43917400-43931600	Weak transcription	Brain Angular Gyrus	brain
14	chr10:43917600-43930800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr10:43917600-43930800	Weak transcription	Fetal Muscle Leg	muscle
16	chr10:43917600-43931600	Weak transcription	Right Ventricle	heart
17	chr10:43920000-43930400	Weak transcription	Liver	Liver
18	chr10:43920000-43930400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr10:43920200-43931600	Weak transcription	Fetal Lung	lung
20	chr10:43921800-43931200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr10:43922800-43930400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:43922800-43930600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr10:43923400-43930400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr10:43923400-43931000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr10:43923600-43928800	Weak transcription	Fetal Stomach	stomach
26	chr10:43923600-43931400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr10:43923800-43930400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr10:43923800-43931600	Weak transcription	Primary T cells from cord blood	blood
29	chr10:43924600-43930600	Weak transcription	Fetal Intestine Large	intestine
30	chr10:43925800-43931600	Weak transcription	Left Ventricle	heart
31	chr10:43926000-43931000	Weak transcription	Adipose Nuclei	Adipose
32	chr10:43926000-43931000	Weak transcription	Placenta	Placenta
33	chr10:43926400-43931400	Weak transcription	Colonic Mucosa	Colon
34	chr10:43926800-43930600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:43927200-43930400	Weak transcription	K562	blood
36	chr10:43927200-43931000	Weak transcription	HSMM	muscle
37	chr10:43927800-43931400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr10:43928000-43928800	Strong transcription	Fetal Intestine Small	intestine
39	chr10:43928200-43930600	Weak transcription	Primary B cells from cord blood	blood
40	chr10:43928200-43930600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr10:43928200-43931000	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr10:43928400-43929800	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr10:43928400-43930400	Weak transcription	Primary monocytes fromperipheralblood	blood

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