Variant report

Variant	rs228874
Chromosome Location	chr17:64496033-64496034
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1473933	0.96[ASN][1000 genomes]
rs1473934	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1514653	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1877846	0.96[ASN][1000 genomes]
rs1877847	0.96[ASN][1000 genomes]
rs1877848	0.94[ASN][1000 genomes]
rs1980118	0.83[ASN][1000 genomes]
rs228870	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs228877	0.96[ASN][1000 genomes]
rs228878	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs228879	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs228881	0.85[EUR][1000 genomes]
rs228884	0.84[EUR][1000 genomes]
rs228887	0.83[EUR][1000 genomes]
rs228888	0.83[EUR][1000 genomes]
rs2361484	0.96[ASN][1000 genomes]
rs2361485	0.96[ASN][1000 genomes]
rs2535659	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2885290	0.96[ASN][1000 genomes]
rs4270211	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4375700	0.96[ASN][1000 genomes]
rs4622543	0.96[ASN][1000 genomes]
rs4791053	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4791054	0.96[ASN][1000 genomes]
rs4791055	0.96[ASN][1000 genomes]
rs4791060	0.83[EUR][1000 genomes]
rs57078491	0.86[AFR][1000 genomes]
rs62070456	0.83[AFR][1000 genomes]
rs6504439	0.96[ASN][1000 genomes]
rs6504440	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7211424	0.96[ASN][1000 genomes]
rs7218008	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7218053	0.96[ASN][1000 genomes]
rs7218480	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7221053	0.84[ASN][1000 genomes]
rs7225362	0.90[ASN][1000 genomes]
rs8064886	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8068988	0.93[ASN][1000 genomes]
rs8068989	0.94[ASN][1000 genomes]
rs8069282	0.88[ASN][1000 genomes]
rs8070470	0.96[ASN][1000 genomes]
rs8079527	0.84[ASN][1000 genomes]
rs9896483	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9896922	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9896956	0.96[ASN][1000 genomes]
rs9897124	0.94[ASN][1000 genomes]
rs9897534	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9898205	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9913336	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9915432	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057876	chr17:64401469-64802341	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv543407	chr17:64401469-64802341	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv457883	chr17:64410915-64510410	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv575897	chr17:64410915-64510410	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv457887	chr17:64410915-64518507	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv575898	chr17:64410915-64518507	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv817351	chr17:64420296-64742555	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv948353	chr17:64454960-64619767	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv948335	chr17:64454960-64745690	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1056765	chr17:64486268-64661890	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:64479000-64499000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr17:64485000-64499200	Weak transcription	Fetal Kidney	kidney
3	chr17:64485800-64498800	Weak transcription	Fetal Intestine Large	intestine
4	chr17:64487600-64505000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr17:64488200-64504400	Weak transcription	Lung	lung
6	chr17:64488600-64503400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr17:64489000-64499400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr17:64489200-64499000	Weak transcription	Fetal Intestine Small	intestine
9	chr17:64489200-64499400	Weak transcription	Pancreas	Pancrea
10	chr17:64489200-64499600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr17:64489200-64501000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr17:64489800-64499200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr17:64490000-64505600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr17:64490400-64499200	Weak transcription	Brain Germinal Matrix	brain
15	chr17:64490400-64503600	Weak transcription	Gastric	stomach
16	chr17:64490400-64520800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr17:64490600-64497200	Weak transcription	Brain Hippocampus Middle	brain
18	chr17:64490600-64497400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr17:64490600-64502600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr17:64490600-64502600	Weak transcription	Small Intestine	intestine
21	chr17:64490600-64503400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr17:64490600-64503600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr17:64490800-64497400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr17:64490800-64499000	Weak transcription	NH-A	brain
25	chr17:64490800-64501000	Weak transcription	HSMMtube	muscle
26	chr17:64490800-64503000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:64490800-64503600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr17:64490800-64505800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr17:64491000-64503200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr17:64491000-64503400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr17:64491000-64517800	Weak transcription	Dnd41	blood
32	chr17:64491200-64499000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:64491200-64499200	Weak transcription	HMEC	breast
34	chr17:64491200-64503000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr17:64491400-64499000	Weak transcription	NHLF	lung
36	chr17:64491400-64503400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr17:64491600-64498200	Weak transcription	Osteobl	bone
38	chr17:64491600-64499000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr17:64491600-64499000	Weak transcription	K562	blood
40	chr17:64492000-64502800	Weak transcription	Ovary	ovary
41	chr17:64492600-64497200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr17:64492600-64497600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr17:64492600-64499000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr17:64492600-64499000	Weak transcription	NHDF-Ad	bronchial
45	chr17:64493000-64499000	Weak transcription	Fetal Brain Male	brain
46	chr17:64493000-64499000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr17:64493200-64496200	Weak transcription	Brain Substantia Nigra	brain
48	chr17:64493200-64499200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:64493200-64499200	Weak transcription	Colon Smooth Muscle	Colon
50	chr17:64493600-64502600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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