Variant report

Variant	rs28407399
Chromosome Location	chr4:74448433-74448434
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10004505	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10011419	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10019146	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10019320	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021827	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028196	0.87[EUR][1000 genomes]
rs10028276	0.87[EUR][1000 genomes]
rs10029673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074085	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10805065	0.87[EUR][1000 genomes]
rs10938085	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10938086	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11728915	0.83[EUR][1000 genomes]
rs1247651	0.95[ASN][1000 genomes]
rs1247668	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1247670	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1247671	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12503916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508661	0.87[EUR][1000 genomes]
rs12508974	0.87[EUR][1000 genomes]
rs12510629	0.87[EUR][1000 genomes]
rs13103378	0.87[EUR][1000 genomes]
rs13115877	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120998	0.87[EUR][1000 genomes]
rs13133747	0.88[EUR][1000 genomes]
rs13144296	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13144390	0.81[EUR][1000 genomes]
rs1528915	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528916	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528917	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528918	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528924	0.87[EUR][1000 genomes]
rs1569204	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16849628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849659	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849677	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849727	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17192413	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1745300	0.85[AMR][1000 genomes]
rs17805623	0.86[EUR][1000 genomes]
rs2008288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178292	0.87[EUR][1000 genomes]
rs28450939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28562313	0.80[AFR][1000 genomes]
rs28612539	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28658027	0.82[EUR][1000 genomes]
rs28693538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28838047	0.83[EUR][1000 genomes]
rs34123018	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34238679	0.86[EUR][1000 genomes]
rs34773614	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34832471	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34859660	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756073	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4438732	0.87[EUR][1000 genomes]
rs4694173	0.87[EUR][1000 genomes]
rs4694626	0.81[EUR][1000 genomes]
rs56011127	0.87[EUR][1000 genomes]
rs56384466	0.87[EUR][1000 genomes]
rs6446941	0.87[EUR][1000 genomes]
rs6837506	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838329	0.84[EUR][1000 genomes]
rs72647083	0.86[EUR][1000 genomes]
rs72649103	0.85[EUR][1000 genomes]
rs7665563	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665972	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667019	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667185	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674913	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676460	0.82[EUR][1000 genomes]
rs7676850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687216	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7695792	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695946	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696502	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990707	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9997572	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9999939	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1792624	chr4:74437054-74453857	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74438000-74464800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:74439800-74448600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:74440200-74449000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:74440200-74449600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:74440200-74451200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:74440200-74455200	Weak transcription	Fetal Intestine Small	intestine
7	chr4:74440200-74457400	Weak transcription	Pancreas	Pancrea
8	chr4:74440200-74472600	Weak transcription	Gastric	stomach
9	chr4:74441200-74464800	Weak transcription	Placenta	Placenta
10	chr4:74442200-74450200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:74442600-74449400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:74442800-74448800	Weak transcription	HMEC	breast
13	chr4:74443600-74455400	Weak transcription	Stomach Mucosa	stomach
14	chr4:74446200-74456000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:74446400-74451000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:74447000-74449400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:74447000-74456000	Strong transcription	Fetal Thymus	thymus
18	chr4:74447400-74449000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:74447600-74448600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:74447600-74448800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:74447600-74449400	Weak transcription	Thymus	Thymus
22	chr4:74447600-74455000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:74447600-74463400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:74448000-74449200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:74448200-74449200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr4:74448400-74448800	Strong transcription	Fetal Intestine Large	intestine

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