Variant report

Variant	rs28798461
Chromosome Location	chr4:99359533-99359534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10002767	0.82[AMR][1000 genomes]
rs10003618	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10010135	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10017792	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10022966	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10025306	0.80[AMR][1000 genomes]
rs10030765	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12501972	0.97[ASN][1000 genomes]
rs12503056	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12505246	0.80[AMR][1000 genomes]
rs12508322	0.88[ASN][1000 genomes]
rs17027564	0.80[AMR][1000 genomes]
rs17027603	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1913488	0.97[ASN][1000 genomes]
rs2063745	0.80[AMR][1000 genomes]
rs2090118	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28416087	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28568441	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28666485	0.81[EUR][1000 genomes]
rs28733733	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34491917	0.80[AMR][1000 genomes]
rs3822115	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4699342	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4699631	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4699632	0.80[AMR][1000 genomes]
rs6811725	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6813960	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6834829	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6835676	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845766	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73832309	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7664210	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7673119	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7675605	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7676060	0.80[AMR][1000 genomes]
rs7676285	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99307000-99366200	Weak transcription	Fetal Brain Male	brain
2	chr4:99308600-99363200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:99325800-99367000	Weak transcription	Right Ventricle	heart
4	chr4:99334400-99361800	Weak transcription	Aorta	Aorta
5	chr4:99334400-99364600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:99334400-99366000	Weak transcription	Psoas Muscle	Psoas
7	chr4:99334400-99367400	Weak transcription	Small Intestine	intestine
8	chr4:99334400-99368800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:99336400-99365000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:99337200-99363200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:99337600-99369800	Weak transcription	Fetal Heart	heart
12	chr4:99338400-99363200	Weak transcription	Spleen	Spleen
13	chr4:99339000-99363200	Weak transcription	Colonic Mucosa	Colon
14	chr4:99339000-99370200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:99340800-99370600	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:99341200-99365000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:99342600-99366600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:99342800-99361000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:99342800-99367400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr4:99342800-99370000	Weak transcription	Placenta	Placenta
21	chr4:99343000-99363200	Weak transcription	HUVEC	blood vessel
22	chr4:99343000-99368000	Weak transcription	Gastric	stomach
23	chr4:99344200-99361800	Weak transcription	Lung	lung
24	chr4:99344200-99366200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:99345000-99367200	Weak transcription	GM12878-XiMat	blood
26	chr4:99346400-99371200	Weak transcription	Fetal Brain Female	brain
27	chr4:99346600-99365600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:99346800-99363000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:99347600-99361800	Weak transcription	Fetal Intestine Small	intestine
30	chr4:99351600-99365200	Weak transcription	Stomach Mucosa	stomach
31	chr4:99352200-99365200	Weak transcription	HepG2	liver
32	chr4:99352200-99366800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr4:99352600-99365200	Strong transcription	Dnd41	blood
34	chr4:99352600-99366200	Weak transcription	NHDF-Ad	bronchial
35	chr4:99353200-99367000	Weak transcription	A549	lung
36	chr4:99354200-99359600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:99355000-99365600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:99355000-99366400	Strong transcription	Primary B cells from cord blood	blood
39	chr4:99355200-99359600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr4:99355200-99359800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:99355200-99361800	Strong transcription	HSMM	muscle
42	chr4:99355200-99365600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:99355400-99361200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr4:99355400-99365800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:99355400-99366600	Strong transcription	Fetal Thymus	thymus
46	chr4:99355600-99365800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:99355800-99361200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:99355800-99363200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:99355800-99367200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr4:99356200-99362600	Weak transcription	Brain Germinal Matrix	brain

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