Variant report

Variant	rs12501397
Chromosome Location	chr4:152171486-152171487
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10006091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10011948	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015834	0.86[EUR][1000 genomes]
rs10016704	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10019075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031618	0.80[AMR][1000 genomes]
rs10031902	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10857257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099801	0.93[EUR][1000 genomes]
rs11099802	0.88[EUR][1000 genomes]
rs11721421	0.87[EUR][1000 genomes]
rs11726496	0.88[EUR][1000 genomes]
rs11729901	0.92[EUR][1000 genomes]
rs11730707	0.93[EUR][1000 genomes]
rs11733473	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733501	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733600	0.88[EUR][1000 genomes]
rs11734518	0.88[EUR][1000 genomes]
rs11734727	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735681	0.87[EUR][1000 genomes]
rs12505382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12508449	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17590780	0.88[EUR][1000 genomes]
rs2291978	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407166	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28650996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28651657	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28767036	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35245353	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3990708	0.88[EUR][1000 genomes]
rs4339187	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4417949	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4473634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55812154	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55855806	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55869644	0.88[EUR][1000 genomes]
rs55905531	0.88[EUR][1000 genomes]
rs56220030	0.86[EUR][1000 genomes]
rs62328350	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328351	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328353	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535782	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535785	0.88[EUR][1000 genomes]
rs6823844	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824195	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6844983	0.91[EUR][1000 genomes]
rs6849871	0.88[EUR][1000 genomes]
rs6849875	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6851493	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72725927	0.88[EUR][1000 genomes]
rs7663659	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7665657	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695360	0.92[EUR][1000 genomes]
rs9985620	0.82[ASN][1000 genomes]
rs9990564	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9994652	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9996742	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9997461	0.93[EUR][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	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152130200-152187800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:152149200-152172000	Weak transcription	Left Ventricle	heart
3	chr4:152149200-152185200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:152149200-152197600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:152149600-152173000	Weak transcription	Right Atrium	heart
6	chr4:152156000-152179800	Weak transcription	Fetal Stomach	stomach
7	chr4:152158800-152178800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:152158800-152181800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:152160600-152172000	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:152163800-152172000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:152164800-152176800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:152165400-152171800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:152165400-152189000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:152167000-152171600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:152167400-152172800	Enhancers	HepG2	liver
16	chr4:152168200-152173400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:152169400-152176600	Weak transcription	Fetal Intestine Large	intestine
18	chr4:152169600-152176600	Weak transcription	Fetal Intestine Small	intestine
19	chr4:152170000-152173000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:152170800-152171800	Weak transcription	Liver	Liver
21	chr4:152171000-152171600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr4:152171000-152173600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr4:152171000-152173800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:152171000-152175200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr4:152171200-152172000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:152171200-152173400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr4:152171200-152173400	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr4:152171400-152172400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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