Variant report

Variant	rs28555361
Chromosome Location	chr17:17934026-17934027
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17927067..17930753-chr17:17932450..17937631,4	MCF-7	breast:
2	chr17:17932163..17934302-chr17:17935217..17938376,3	K562	blood:

Variant related genes	Relation type
ENSG00000171953	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11650021	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11871231	0.80[EUR][1000 genomes]
rs12150369	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12939020	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12940282	0.84[AMR][1000 genomes]
rs28537385	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955350	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955353	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955354	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955355	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955356	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955357	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955358	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955359	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955368	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2955370	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955372	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2955377	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2955378	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2955380	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955381	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2955383	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2955384	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2955385	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4072738	0.80[EUR][1000 genomes]
rs4072739	0.80[EUR][1000 genomes]
rs4365348	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4368210	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4459604	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4506969	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4584886	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4643387	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4924832	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4925135	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4925136	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62072050	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6502631	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6502632	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6502633	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6502634	0.85[AMR][1000 genomes]
rs7207461	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7207821	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7209003	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7210400	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7212167	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7215524	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7219324	0.81[EUR][1000 genomes]
rs7223696	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7224047	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7406982	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7503738	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8069811	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8070731	0.80[AMR][1000 genomes]
rs8071238	0.84[AMR][1000 genomes]
rs8075189	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8080602	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8082590	0.84[AMR][1000 genomes]
rs9894138	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9896837	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9897761	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9911850	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9912096	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9913277	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17906200-17941400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr17:17908800-17941200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr17:17916400-17936600	Weak transcription	Fetal Kidney	kidney
4	chr17:17917400-17936600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr17:17921000-17940000	Weak transcription	Fetal Brain Male	brain
6	chr17:17922200-17941000	Weak transcription	Small Intestine	intestine
7	chr17:17923800-17941400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr17:17925200-17941000	Weak transcription	Colon Smooth Muscle	Colon
9	chr17:17925200-17941000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr17:17925400-17939000	Weak transcription	Gastric	stomach
11	chr17:17925400-17941000	Weak transcription	Colonic Mucosa	Colon
12	chr17:17925400-17941200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr17:17927800-17940800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr17:17929600-17936600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr17:17930000-17934600	Weak transcription	HUVEC	blood vessel
16	chr17:17930000-17935200	Weak transcription	NH-A	brain
17	chr17:17930000-17941000	Weak transcription	Brain Anterior Caudate	brain
18	chr17:17930200-17935000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr17:17930200-17935000	Weak transcription	HSMM	muscle
20	chr17:17930200-17935200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:17930200-17935200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr17:17930200-17935200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:17930200-17935200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr17:17930200-17935200	Weak transcription	NHLF	lung
25	chr17:17930200-17936600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr17:17930200-17941000	Weak transcription	Brain Angular Gyrus	brain
27	chr17:17930200-17941200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr17:17930200-17941200	Weak transcription	Brain Substantia Nigra	brain
29	chr17:17930200-17941400	Weak transcription	HSMMtube	muscle
30	chr17:17930200-17942000	Weak transcription	Aorta	Aorta
31	chr17:17930400-17935200	Weak transcription	Osteobl	bone
32	chr17:17930400-17939000	Weak transcription	Brain Germinal Matrix	brain
33	chr17:17930800-17935200	Weak transcription	A549	lung
34	chr17:17931000-17934800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr17:17931000-17935200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr17:17931000-17936400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr17:17931000-17936600	Weak transcription	Liver	Liver
38	chr17:17931000-17940600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr17:17931200-17940600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr17:17931200-17941000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr17:17931400-17935400	Weak transcription	Right Atrium	heart
42	chr17:17931400-17939000	Weak transcription	Fetal Lung	lung
43	chr17:17931600-17935000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr17:17931600-17935200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr17:17931600-17935200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr17:17931600-17935200	Weak transcription	Spleen	Spleen
47	chr17:17931600-17936600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr17:17931600-17936600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr17:17931600-17936600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr17:17931600-17936600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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