Variant report

Variant	rs28893880
Chromosome Location	chr4:100839643-100839644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:100837131..100839848-chr4:100866356..100868236,2	K562	blood:
2	chr4:100837896..100840734-chr4:100841683..100843412,2	MCF-7	breast:
3	chr4:100838599..100840413-chr4:100870184..100872469,2	MCF-7	breast:
4	chr4:100829396..100833198-chr4:100836822..100839868,3	MCF-7	breast:
5	chr4:100837674..100840166-chr4:100869128..100872455,4	K562	blood:
6	chr4:100834943..100837070-chr4:100838734..100840986,2	K562	blood:

Variant related genes	Relation type
ENSG00000245322	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000164031	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10001730	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10002820	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10014424	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];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10016741	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10018937	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10461176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1365494	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17029542	1.00[JPT][hapmap]
rs17029575	0.82[ASN][1000 genomes]
rs17029577	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17029592	0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]
rs17029594	0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[ASN][1000 genomes]
rs17029601	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17029606	1.00[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17029641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17029667	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17029681	0.93[ASN][1000 genomes]
rs17029696	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17029698	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17029717	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2282587	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2298734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28375729	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs28445732	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28497573	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28553972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28561548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28566137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28604943	1.00[ASN][1000 genomes]
rs28635099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2866175	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[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];0.91[ASN][1000 genomes]
rs28824275	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3737485	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3775510	0.94[ASN][1000 genomes]
rs4463078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56996205	0.80[ASN][1000 genomes]
rs57001633	0.80[ASN][1000 genomes]
rs57238114	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs57862852	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs58512740	0.82[ASN][1000 genomes]
rs59439986	0.86[ASN][1000 genomes]
rs59768994	1.00[ASN][1000 genomes]
rs60203069	1.00[ASN][1000 genomes]
rs60584294	0.82[ASN][1000 genomes]
rs60899666	0.82[ASN][1000 genomes]
rs60994806	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs61229555	0.93[ASN][1000 genomes]
rs62305048	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100815600-100840000	Weak transcription	Small Intestine	intestine
2	chr4:100816000-100839800	Weak transcription	Esophagus	oesophagus
3	chr4:100816000-100867000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:100816000-100867000	Weak transcription	Lung	lung
5	chr4:100816200-100839800	Weak transcription	Aorta	Aorta
6	chr4:100816200-100840200	Weak transcription	Colonic Mucosa	Colon
7	chr4:100816200-100842200	Weak transcription	Pancreas	Pancrea
8	chr4:100816200-100851400	Weak transcription	A549	lung
9	chr4:100816200-100851600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:100816200-100853600	Weak transcription	NHLF	lung
11	chr4:100816200-100866200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:100816400-100845800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:100816600-100839800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:100816600-100841800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:100816600-100843800	Weak transcription	Right Ventricle	heart
16	chr4:100819600-100839800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr4:100820000-100866200	Weak transcription	Fetal Heart	heart
18	chr4:100823600-100845600	Weak transcription	Hela-S3	cervix
19	chr4:100823800-100839800	Weak transcription	Ovary	ovary
20	chr4:100824000-100865800	Weak transcription	Psoas Muscle	Psoas
21	chr4:100824400-100847000	Weak transcription	Brain Angular Gyrus	brain
22	chr4:100824400-100866000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:100824800-100854200	Weak transcription	Brain Anterior Caudate	brain
24	chr4:100826200-100844000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:100827600-100856400	Weak transcription	Brain Substantia Nigra	brain
26	chr4:100827800-100839800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:100828800-100866200	Weak transcription	Stomach Mucosa	stomach
28	chr4:100829200-100856400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:100829200-100866600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:100829400-100839800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:100829400-100852600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:100829400-100856200	Weak transcription	HepG2	liver
33	chr4:100829600-100866200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:100829800-100840000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr4:100836000-100842600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:100836200-100846600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:100836600-100839800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:100836600-100840600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:100836600-100856800	Weak transcription	Spleen	Spleen
40	chr4:100836800-100847400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr4:100836800-100851800	Strong transcription	Dnd41	blood
42	chr4:100837400-100840400	Strong transcription	Thymus	Thymus
43	chr4:100837600-100842000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr4:100837600-100852600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:100838000-100840400	Strong transcription	Left Ventricle	heart
46	chr4:100838200-100840200	Strong transcription	HMEC	breast
47	chr4:100838200-100840800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:100838200-100850200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr4:100838400-100839800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
50	chr4:100838400-100839800	Strong transcription	Duodenum Mucosa	Duodenum

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