Variant report

Variant	rs2838775
Chromosome Location	chr21:46511411-46511412
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46493665..46495274-chr21:46510710..46513297,2	MCF-7	breast:
2	chr21:46509836..46512194-chr21:46536516..46538934,2	K562	blood:
3	chr21:46510275..46513095-chr21:46517504..46519501,2	MCF-7	breast:
4	chr21:46510851..46513233-chr21:46534115..46536382,2	K562	blood:

Variant related genes	Relation type
ENSG00000235374	Chromatin interaction
ENSG00000267857	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11908769	0.89[AFR][1000 genomes]
rs11911694	0.89[AFR][1000 genomes]
rs17004737	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17004740	0.89[AFR][1000 genomes]
rs17004746	0.89[AFR][1000 genomes]
rs2032253	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838772	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2838777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838785	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877003	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3171490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373249	1.00[ASN][1000 genomes]
rs375621	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs387536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs406923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs407157	1.00[ASN][1000 genomes]
rs412431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs420499	1.00[CEU][hapmap]
rs422205	0.93[ASN][1000 genomes]
rs423892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs425176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs437833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs444789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs451550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73230653	1.00[AMR][1000 genomes]
rs73230658	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73230662	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73230667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230679	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230681	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8133767	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]

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	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	nsv3541	chr21:46496415-46536629	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46496200-46511600	Weak transcription	Fetal Intestine Small	intestine
2	chr21:46496400-46513000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr21:46496600-46511600	Weak transcription	Brain Hippocampus Middle	brain
4	chr21:46496600-46512000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr21:46496600-46516200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr21:46498600-46513000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr21:46499000-46522200	Weak transcription	NHDF-Ad	bronchial
8	chr21:46500000-46522200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr21:46501600-46513000	Weak transcription	Brain Anterior Caudate	brain
10	chr21:46502000-46515400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr21:46502000-46516000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr21:46503000-46522200	Weak transcription	Brain Angular Gyrus	brain
13	chr21:46503200-46516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr21:46503200-46516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr21:46503800-46513000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr21:46506600-46513000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr21:46506600-46521400	Weak transcription	NHEK	skin
18	chr21:46507600-46513000	Weak transcription	Esophagus	oesophagus
19	chr21:46507600-46513600	Weak transcription	Thymus	Thymus
20	chr21:46507600-46515200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr21:46508000-46513000	Weak transcription	Fetal Thymus	thymus
22	chr21:46508200-46511600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr21:46508200-46513000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr21:46508400-46513200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr21:46509000-46512000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr21:46509000-46512800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr21:46509000-46513000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr21:46509000-46513000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr21:46509000-46513000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr21:46509200-46511600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr21:46509200-46511600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr21:46509200-46512400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr21:46509200-46512800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr21:46509400-46524000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr21:46509800-46512200	Enhancers	Fetal Lung	lung
36	chr21:46509800-46513800	Enhancers	Fetal Brain Female	brain
37	chr21:46510000-46513200	Weak transcription	Dnd41	blood
38	chr21:46510200-46514800	Enhancers	Fetal Brain Male	brain
39	chr21:46510200-46515600	Weak transcription	K562	blood
40	chr21:46510400-46512800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr21:46510400-46513000	Weak transcription	Primary T cells from cord blood	blood
42	chr21:46510400-46515200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr21:46510600-46511800	Enhancers	Colon Smooth Muscle	Colon
44	chr21:46510600-46512200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr21:46510600-46513200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr21:46510600-46519200	Enhancers	Primary B cells from peripheral blood	blood
47	chr21:46510800-46511600	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr21:46510800-46513000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr21:46510800-46513000	Weak transcription	Aorta	Aorta
50	chr21:46511000-46511800	Enhancers	Colonic Mucosa	Colon

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