Variant report

Variant	rs2838679
Chromosome Location	chr21:46191447-46191448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55277286..55278001-chr21:46191224..46192040,2	MCF-7	breast:
2	chr21:46182776..46184894-chr21:46189262..46192289,3	K562	blood:
3	chr21:46191384..46193561-chr21:46204245..46206400,3	MCF-7	breast:
4	chr21:46191363..46195338-chr21:46195868..46201575,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13047692	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13047718	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13051119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13433413	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17004706	1.00[ASW][hapmap];0.90[MEX][hapmap]
rs17004710	1.00[ASW][hapmap]
rs2294158	0.98[ASN][1000 genomes]
rs2838676	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2838677	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2838693	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838697	0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838698	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs2838700	0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs34875321	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788138	0.97[ASN][1000 genomes]
rs4818731	0.96[ASN][1000 genomes]
rs4818976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818977	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72613649	0.94[ASN][1000 genomes]
rs8131444	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8132011	0.81[ASN][1000 genomes]
rs873317	1.00[ASW][hapmap]
rs9306115	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9306116	0.85[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs9637189	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9808690	0.91[MEX][hapmap]
rs9977465	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9977676	0.97[ASN][1000 genomes]
rs9978131	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9981344	0.95[CHB][hapmap];0.95[JPT][hapmap]

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	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46185800-46192600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr21:46185800-46199600	Weak transcription	Stomach Mucosa	stomach
3	chr21:46186200-46199400	Weak transcription	Right Atrium	heart
4	chr21:46187000-46193000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr21:46187000-46193200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr21:46187000-46195400	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr21:46187000-46213000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr21:46187200-46194600	Weak transcription	NHDF-Ad	bronchial
9	chr21:46187200-46197800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr21:46187600-46196200	Strong transcription	Thymus	Thymus
11	chr21:46187800-46196600	Strong transcription	Right Ventricle	heart
12	chr21:46187800-46199000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr21:46187800-46206200	Strong transcription	Fetal Thymus	thymus
14	chr21:46188000-46193000	Strong transcription	Fetal Intestine Small	intestine
15	chr21:46188000-46193400	Strong transcription	Lung	lung
16	chr21:46188000-46195800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr21:46188000-46196800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr21:46188000-46198600	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr21:46188000-46198600	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr21:46188000-46198800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr21:46188000-46199000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr21:46188000-46201600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr21:46188000-46203000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr21:46188000-46203200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr21:46188000-46208000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr21:46188200-46193400	Strong transcription	Placenta	Placenta
27	chr21:46188200-46195000	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr21:46188200-46197000	Strong transcription	Fetal Brain Female	brain
29	chr21:46188200-46197200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr21:46188200-46197200	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr21:46188200-46197400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr21:46188200-46198800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr21:46188200-46199000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr21:46188200-46199800	Strong transcription	Primary T cells from cord blood	blood
35	chr21:46188200-46201600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr21:46188400-46193400	Strong transcription	Esophagus	oesophagus
37	chr21:46188400-46193400	Strong transcription	Fetal Muscle Leg	muscle
38	chr21:46188400-46194800	Strong transcription	Rectal Smooth Muscle	rectum
39	chr21:46188400-46196000	Strong transcription	Ovary	ovary
40	chr21:46188400-46196800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr21:46188400-46197000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr21:46188400-46198600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr21:46188400-46198600	Strong transcription	Adipose Nuclei	Adipose
44	chr21:46188400-46199400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr21:46188600-46197400	Strong transcription	Liver	Liver
46	chr21:46188600-46198400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr21:46188600-46200200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr21:46188600-46201600	Strong transcription	Fetal Stomach	stomach
49	chr21:46188600-46208000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr21:46188800-46192000	Strong transcription	Fetal Muscle Trunk	muscle

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