Variant report

Variant	rs6554966
Chromosome Location	chr5:17057763-17057764
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:17055618..17058211-chr5:17065724..17068403,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11133881	0.81[EUR][1000 genomes]
rs11744180	0.80[ASN][1000 genomes]
rs11948837	0.86[ASN][1000 genomes]
rs12186388	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12186858	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12187047	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1842759	0.91[ASN][1000 genomes]
rs2086606	0.91[ASN][1000 genomes]
rs2086608	0.91[ASN][1000 genomes]
rs28669748	0.87[ASN][1000 genomes]
rs3860140	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4072898	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4072899	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4607350	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4701678	0.81[ASN][1000 genomes]
rs4701680	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4702190	0.81[ASN][1000 genomes]
rs4702192	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58076264	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs58236592	0.85[ASN][1000 genomes]
rs58425041	0.83[ASN][1000 genomes]
rs60901893	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62348834	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62350295	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6554964	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554965	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6862915	0.91[ASN][1000 genomes]
rs6884918	0.87[ASN][1000 genomes]
rs6890007	0.88[ASN][1000 genomes]
rs6897712	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898175	0.80[ASN][1000 genomes]
rs72636107	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72636108	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72734394	0.91[ASN][1000 genomes]
rs7706695	0.90[ASN][1000 genomes]
rs7710867	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7716749	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7723238	0.87[ASN][1000 genomes]
rs7727307	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7730952	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7737397	0.91[ASN][1000 genomes]
rs9687340	0.90[ASN][1000 genomes]
rs9688197	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv3510797	chr5:16966764-17125849	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3510798	chr5:16966764-17125849	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1795984	chr5:16973769-17078295	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1017222	chr5:17001819-17133274	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1021972	chr5:17011758-17091878	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1026025	chr5:17039665-17195440	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17052800-17058000	Enhancers	Fetal Brain Male	brain
2	chr5:17055600-17060000	Enhancers	Stomach Mucosa	stomach
3	chr5:17055800-17058000	Enhancers	Adipose Nuclei	Adipose
4	chr5:17056000-17057800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr5:17056000-17058000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr5:17056000-17058000	Enhancers	NHEK	skin
7	chr5:17056200-17057800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:17056200-17057800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr5:17056200-17057800	Enhancers	Fetal Brain Female	brain
10	chr5:17056200-17058000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:17056200-17058000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:17056200-17058200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:17056200-17058200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:17056400-17058000	Enhancers	Pancreas	Pancrea
15	chr5:17056600-17057800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:17056600-17058400	Enhancers	Fetal Stomach	stomach
17	chr5:17056600-17058600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:17056600-17062200	Weak transcription	Placenta	Placenta
19	chr5:17056800-17062200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:17056800-17064600	Weak transcription	Ovary	ovary
21	chr5:17057200-17058000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:17057200-17058200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:17057200-17058200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr5:17057200-17058200	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr5:17057400-17057800	Enhancers	Colon Smooth Muscle	Colon
26	chr5:17057400-17057800	Enhancers	Spleen	Spleen
27	chr5:17057400-17057800	Enhancers	HMEC	breast
28	chr5:17057400-17058000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:17057400-17058000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:17057400-17058000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr5:17057400-17058000	Enhancers	Brain Angular Gyrus	brain
32	chr5:17057400-17058000	Enhancers	Brain Cingulate Gyrus	brain
33	chr5:17057400-17058000	Enhancers	Duodenum Mucosa	Duodenum
34	chr5:17057400-17058000	Enhancers	Fetal Lung	lung
35	chr5:17057400-17058000	Enhancers	Small Intestine	intestine
36	chr5:17057400-17058200	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr5:17057400-17058600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:17057400-17058600	Enhancers	HUVEC	blood vessel
39	chr5:17057600-17057800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:17057600-17057800	Enhancers	Fetal Muscle Leg	muscle
41	chr5:17057600-17057800	Enhancers	NHDF-Ad	bronchial
42	chr5:17057600-17058000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:17057600-17058000	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr5:17057600-17058000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:17057600-17058000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:17057600-17058000	Enhancers	Stomach Smooth Muscle	stomach
47	chr5:17057600-17058000	Flanking Active TSS	A549	lung
48	chr5:17057600-17058000	Enhancers	NH-A	brain
49	chr5:17057600-17058200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:17057600-17058200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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