Variant report

Variant	rs28553972
Chromosome Location	chr4:100866128-100866129
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:100799869..100822436-chr4:100866015..100873106,54	K562	blood:
2	chr4:100813266..100817175-chr4:100865527..100871657,11	MCF-7	breast:
3	chr4:100810623..100827791-chr4:100865444..100874425,55	K562	blood:
4	chr4:100850716..100855335-chr4:100865818..100872882,15	K562	blood:

Variant related genes	Relation type
ENSG00000164031	Chromatin interaction
ENSG00000109270	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10001730	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10002820	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10014424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10016741	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10018937	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10461176	0.93[ASN][1000 genomes]
rs1365494	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17029575	0.80[ASN][1000 genomes]
rs17029577	0.80[ASN][1000 genomes]
rs17029592	0.80[ASN][1000 genomes]
rs17029594	0.84[ASN][1000 genomes]
rs17029601	0.89[AFR][1000 genomes]
rs17029606	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17029641	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17029667	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs17029681	0.94[ASN][1000 genomes]
rs17029696	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17029698	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17029717	0.91[ASN][1000 genomes]
rs2282587	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2298734	0.96[ASN][1000 genomes]
rs28375729	1.00[ASN][1000 genomes]
rs28445732	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28497573	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28561548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28566137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28604943	0.98[ASN][1000 genomes]
rs28635099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2866175	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28705829	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs28709045	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28824275	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28893880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3737485	0.80[ASN][1000 genomes]
rs3775510	0.92[ASN][1000 genomes]
rs4463078	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57238114	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs57862852	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs58512740	0.80[ASN][1000 genomes]
rs59439986	0.87[ASN][1000 genomes]
rs59768994	0.98[ASN][1000 genomes]
rs60203069	0.98[ASN][1000 genomes]
rs60584294	0.80[ASN][1000 genomes]
rs60899666	0.80[ASN][1000 genomes]
rs60994806	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs61229555	0.94[ASN][1000 genomes]
rs62305048	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879661	chr4:100805207-100869635	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv879662	chr4:100849466-100876648	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100816000-100867000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:100816000-100867000	Weak transcription	Lung	lung
3	chr4:100816200-100866200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:100820000-100866200	Weak transcription	Fetal Heart	heart
5	chr4:100828800-100866200	Weak transcription	Stomach Mucosa	stomach
6	chr4:100829200-100866600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:100829600-100866200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:100840200-100867000	Weak transcription	Gastric	stomach
9	chr4:100840400-100866800	Weak transcription	Aorta	Aorta
10	chr4:100840400-100867000	Weak transcription	Esophagus	oesophagus
11	chr4:100847800-100866200	Weak transcription	HSMMtube	muscle
12	chr4:100848400-100866200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:100856800-100866200	Weak transcription	NH-A	brain
14	chr4:100857000-100866200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:100857200-100866200	Weak transcription	Thymus	Thymus
16	chr4:100857200-100866200	Weak transcription	Spleen	Spleen
17	chr4:100857800-100866200	Weak transcription	HMEC	breast
18	chr4:100857800-100866400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:100858000-100866200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr4:100858000-100866200	Weak transcription	Fetal Brain Female	brain
21	chr4:100858000-100866200	Weak transcription	Fetal Thymus	thymus
22	chr4:100859000-100866200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:100859000-100866200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:100859000-100867000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:100860400-100866800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr4:100862000-100866600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr4:100862200-100866200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:100862400-100866200	Enhancers	Primary T cells from cord blood	blood
29	chr4:100864200-100866200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:100864200-100866400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr4:100864200-100866800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:100864200-100866800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr4:100864400-100866200	Enhancers	NHEK	skin
34	chr4:100864400-100866600	Enhancers	Brain Cingulate Gyrus	brain
35	chr4:100864600-100866200	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr4:100864600-100866600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr4:100864800-100866200	Enhancers	Adipose Nuclei	Adipose
38	chr4:100864800-100866400	Enhancers	Colon Smooth Muscle	Colon
39	chr4:100864800-100866600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr4:100864800-100866800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr4:100864800-100866800	Enhancers	Primary B cells from peripheral blood	blood
42	chr4:100864800-100867000	Enhancers	Small Intestine	intestine
43	chr4:100865000-100866200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:100865000-100866200	Weak transcription	HSMM	muscle
45	chr4:100865000-100866600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:100865200-100866200	Enhancers	Primary B cells from cord blood	blood
47	chr4:100865200-100868000	Active TSS	GM12878-XiMat	blood
48	chr4:100865400-100866200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:100865400-100866200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr4:100865400-100866400	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links