Variant report

Variant	rs9893296
Chromosome Location	chr17:19880120-19880121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:19834831..19836752-chr17:19879517..19881756,2	MCF-7	breast:
2	chr17:19769754..19773058-chr17:19878983..19882883,4	MCF-7	breast:
3	chr17:19879148..19882537-chr17:19911149..19913260,3	MCF-7	breast:
4	chr17:19864763..19867496-chr17:19878736..19880749,2	K562	blood:
5	chr17:19769588..19772074-chr17:19879592..19882526,4	MCF-7	breast:
6	chr17:19873620..19876198-chr17:19879057..19880667,2	MCF-7	breast:
7	chr17:19861091..19865827-chr17:19879221..19882528,6	MCF-7	breast:
8	chr17:19878871..19883594-chr17:20057277..20060362,4	K562	blood:
9	chr17:19877816..19880542-chr17:20058157..20059665,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261033	Chromatin interaction
ENSG00000083290	Chromatin interaction
ENSG00000108599	Chromatin interaction
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1638526	0.86[ASN][1000 genomes]
rs16960545	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16960602	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2072337	0.90[ASN][1000 genomes]
rs28410781	1.00[AMR][1000 genomes]
rs28424266	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581607	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28653561	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28767032	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28830504	1.00[AMR][1000 genomes]
rs28865331	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3909257	1.00[AMR][1000 genomes]
rs4141185	0.90[ASN][1000 genomes]
rs59294806	0.80[ASN][1000 genomes]
rs6587207	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6587208	1.00[AMR][1000 genomes]
rs7207459	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7207702	1.00[AMR][1000 genomes]
rs7208033	1.00[AMR][1000 genomes]
rs7209653	0.86[ASN][1000 genomes]
rs7210076	1.00[AMR][1000 genomes]
rs7210751	1.00[AMR][1000 genomes]
rs7214107	1.00[AMR][1000 genomes]
rs7215639	1.00[EUR][1000 genomes]
rs7215769	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7217387	1.00[AMR][1000 genomes]
rs7217862	1.00[AMR][1000 genomes]
rs7217868	1.00[AMR][1000 genomes]
rs7217928	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7218251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7218919	1.00[AMR][1000 genomes]
rs7219153	1.00[AMR][1000 genomes]
rs7219487	1.00[AMR][1000 genomes]
rs7220490	1.00[AMR][1000 genomes]
rs7221669	1.00[AMR][1000 genomes]
rs7223323	1.00[AMR][1000 genomes]
rs7224373	1.00[AMR][1000 genomes]
rs7224419	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7224567	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7224713	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7224875	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73303979	0.90[ASN][1000 genomes]
rs8065122	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8068015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068488	1.00[EUR][1000 genomes]
rs8071670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8079093	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8079487	1.00[EUR][1000 genomes]
rs8080190	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8082671	1.00[AMR][1000 genomes]
rs9889938	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9890105	1.00[AMR][1000 genomes]
rs9891008	1.00[AMR][1000 genomes]
rs9892175	1.00[AMR][1000 genomes]
rs9892271	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9893185	1.00[AMR][1000 genomes]
rs9894666	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9895556	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9896010	1.00[AMR][1000 genomes]
rs9896387	1.00[AMR][1000 genomes]
rs9896499	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9896633	1.00[EUR][1000 genomes]
rs9896641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9897430	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9897607	1.00[AMR][1000 genomes]
rs9898618	1.00[EUR][1000 genomes]
rs9900393	1.00[AMR][1000 genomes]
rs9900441	1.00[AMR][1000 genomes]
rs9900510	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9901294	0.86[ASN][1000 genomes]
rs9901862	1.00[AMR][1000 genomes]
rs9902663	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9903631	1.00[EUR][1000 genomes]
rs9904059	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9908415	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9909011	1.00[AMR][1000 genomes]
rs9909012	1.00[AMR][1000 genomes]
rs9909242	1.00[AMR][1000 genomes]
rs9909544	1.00[AMR][1000 genomes]
rs9911408	1.00[EUR][1000 genomes]
rs9911872	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9912184	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9912648	1.00[EUR][1000 genomes]
rs9912657	1.00[AMR][1000 genomes]
rs9913858	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914328	1.00[AMR][1000 genomes]
rs9914429	1.00[AMR][1000 genomes]
rs9915039	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9915413	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19850600-19880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:19850600-19880200	Weak transcription	Aorta	Aorta
3	chr17:19857400-19880400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:19857600-19880200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr17:19862000-19880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:19862000-19880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr17:19865200-19880200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr17:19869000-19880200	Weak transcription	HSMMtube	muscle
9	chr17:19872000-19880200	Weak transcription	Colonic Mucosa	Colon
10	chr17:19874400-19880400	Weak transcription	Ovary	ovary
11	chr17:19874600-19880600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr17:19875400-19880200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:19877600-19880200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr17:19878000-19880200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:19878400-19880200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr17:19878400-19880200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr17:19878600-19880200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr17:19878600-19880200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr17:19878600-19880200	Enhancers	Colon Smooth Muscle	Colon
20	chr17:19878800-19880200	Enhancers	Primary B cells from peripheral blood	blood
21	chr17:19878800-19880200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr17:19879000-19880200	Enhancers	Primary B cells from cord blood	blood
23	chr17:19879000-19880200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr17:19879000-19880200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr17:19879000-19880200	Enhancers	Brain Substantia Nigra	brain
26	chr17:19879000-19880400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr17:19879200-19880200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr17:19879200-19880200	Enhancers	Brain Cingulate Gyrus	brain
29	chr17:19879200-19881600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr17:19879400-19880200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr17:19879400-19880200	Enhancers	Primary T cells from cord blood	blood
32	chr17:19879400-19880200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr17:19879400-19880200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr17:19879400-19880200	Weak transcription	Fetal Heart	heart
35	chr17:19879400-19880200	Enhancers	Fetal Muscle Trunk	muscle
36	chr17:19879400-19880200	Enhancers	Stomach Mucosa	stomach
37	chr17:19879400-19880200	Enhancers	NH-A	brain
38	chr17:19879400-19880200	Active TSS	Osteobl	bone
39	chr17:19879400-19880400	Enhancers	Spleen	Spleen
40	chr17:19879400-19880400	Flanking Active TSS	Dnd41	blood
41	chr17:19879400-19881400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr17:19879400-19882000	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr17:19879400-19882400	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr17:19879600-19880200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr17:19879600-19880400	Enhancers	Lung	lung
46	chr17:19879600-19880600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr17:19879600-19880600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr17:19879600-19881400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr17:19879600-19881400	Active TSS	A549	lung
50	chr17:19879600-19881400	Active TSS	GM12878-XiMat	blood

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