Variant report

Variant	rs2823003
Chromosome Location	chr21:16375029-16375030
allele	A/G
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	chr21:16374861-16375212	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr21:16374159-16376234	HepG2	liver:	n/a	n/a
3	POLR2A	chr21:16374158-16375040	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
NRIP1	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1041404	0.81[JPT][hapmap]
rs13052079	0.95[ASN][1000 genomes]
rs1997577	0.87[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2178893	0.95[ASN][1000 genomes]
rs2251399	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2822998	0.82[CHD][hapmap]
rs2823002	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2823006	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2823007	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2823009	0.86[EUR][1000 genomes]
rs2823017	0.94[GIH][hapmap];0.93[TSI][hapmap]
rs2823022	0.81[JPT][hapmap]
rs2823026	0.83[GIH][hapmap]
rs2823027	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2823029	0.91[CHB][hapmap]
rs28574812	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517179	0.86[EUR][1000 genomes]
rs6517180	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7280064	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap]
rs7281871	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7282769	0.94[ASN][1000 genomes]
rs7283762	0.88[ASN][1000 genomes]
rs8132398	0.86[TSI][hapmap]
rs9305530	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[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	nsv1060151	chr21:16295713-16435497	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv544378	chr21:16295713-16435497	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv834048	chr21:16324481-16489570	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16340600-16375800	Weak transcription	Right Ventricle	heart
2	chr21:16340800-16375800	Weak transcription	Gastric	stomach
3	chr21:16340800-16375800	Weak transcription	Lung	lung
4	chr21:16340800-16377600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr21:16341200-16388600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr21:16341600-16377000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr21:16358800-16377600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr21:16360400-16380200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr21:16360400-16402600	Weak transcription	Placenta	Placenta
10	chr21:16361800-16375800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr21:16362200-16377600	Weak transcription	Fetal Stomach	stomach
12	chr21:16362200-16385800	Weak transcription	K562	blood
13	chr21:16363400-16383000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr21:16363600-16375800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr21:16363600-16377600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr21:16363600-16377600	Weak transcription	Thymus	Thymus
17	chr21:16363800-16376800	Weak transcription	Dnd41	blood
18	chr21:16364800-16423000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr21:16366000-16379000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr21:16366200-16375800	Weak transcription	Fetal Thymus	thymus
21	chr21:16368600-16414600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr21:16369000-16375800	Weak transcription	HUVEC	blood vessel
23	chr21:16369000-16377600	Weak transcription	NHEK	skin
24	chr21:16369200-16377800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr21:16370200-16383600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr21:16370800-16377400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr21:16371000-16375800	Weak transcription	Right Atrium	heart
28	chr21:16371600-16375800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr21:16371600-16375800	Weak transcription	Left Ventricle	heart
30	chr21:16371600-16375800	Weak transcription	Spleen	Spleen
31	chr21:16372000-16377200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr21:16372200-16379200	Weak transcription	Primary B cells from cord blood	blood
33	chr21:16372400-16375200	Enhancers	Liver	Liver
34	chr21:16372600-16376800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr21:16373000-16375200	Enhancers	NH-A	brain
36	chr21:16373200-16376800	Enhancers	A549	lung
37	chr21:16373400-16379600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr21:16373600-16375200	Enhancers	Psoas Muscle	Psoas
39	chr21:16373600-16375200	Enhancers	Small Intestine	intestine
40	chr21:16373600-16376000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr21:16373600-16377200	Weak transcription	Colon Smooth Muscle	Colon
42	chr21:16373600-16377600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr21:16373600-16377600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr21:16373600-16379000	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr21:16373800-16376600	Weak transcription	HMEC	breast
46	chr21:16373800-16376800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr21:16373800-16376800	Weak transcription	NHDF-Ad	bronchial
48	chr21:16373800-16377200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr21:16374000-16375200	Enhancers	Brain Hippocampus Middle	brain
50	chr21:16374000-16376000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links