Variant report

Variant	rs62417698
Chromosome Location	chr6:88301362-88301363
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:88301149-88301408	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:88300543..88303265-chr6:88372945..88374900,2	K562	blood:
2	chr6:88298942..88303064-chr6:88409165..88412231,4	K562	blood:
3	chr6:88299673..88301546-chr6:89673147..89674942,2	K562	blood:
4	chr6:88299988..88301682-chr6:88305873..88308812,2	K562	blood:
5	chr6:88300267..88302133-chr6:88313231..88315132,2	MCF-7	breast:
6	chr6:88300436..88304356-chr6:88305861..88309850,4	MCF-7	breast:
7	chr6:88300479..88302167-chr6:88410485..88412465,2	MCF-7	breast:
8	chr6:88299553..88301559-chr6:88410382..88412634,2	MCF-7	breast:
9	chr6:88299715..88302499-chr6:88315597..88317409,2	MCF-7	breast:

No data

Variant related genes	Relation type
RARS2	TF binding region
ENSG00000135336	Chromatin interaction
ENSG00000135334	Chromatin interaction
ENSG00000203863	Chromatin interaction
ENSG00000111880	Chromatin interaction

Extended variants
information (count: 173 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:168)

rs_ID	r²[population]
rs13193193	1.00[AFR][1000 genomes]
rs13193303	0.83[EUR][1000 genomes]
rs13193470	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13193703	0.83[EUR][1000 genomes]
rs13193911	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13193927	0.83[EUR][1000 genomes]
rs13196538	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13196755	0.84[EUR][1000 genomes]
rs13197090	0.83[EUR][1000 genomes]
rs13198094	0.84[EUR][1000 genomes]
rs13200106	0.83[EUR][1000 genomes]
rs13202825	0.83[EUR][1000 genomes]
rs13203056	0.83[EUR][1000 genomes]
rs13203649	0.84[EUR][1000 genomes]
rs13203790	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13203957	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13204592	0.83[EUR][1000 genomes]
rs13204861	0.83[EUR][1000 genomes]
rs13206536	0.84[EUR][1000 genomes]
rs13206957	0.84[EUR][1000 genomes]
rs13208201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13208550	0.83[EUR][1000 genomes]
rs13208933	0.83[EUR][1000 genomes]
rs13210643	0.83[EUR][1000 genomes]
rs13211439	0.83[EUR][1000 genomes]
rs13211833	1.00[AFR][1000 genomes]
rs13212076	0.83[EUR][1000 genomes]
rs13212089	0.83[EUR][1000 genomes]
rs13213285	0.84[EUR][1000 genomes]
rs13215013	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13215887	0.83[EUR][1000 genomes]
rs13216482	1.00[AFR][1000 genomes]
rs13216724	0.83[EUR][1000 genomes]
rs13216727	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13219631	1.00[AFR][1000 genomes]
rs16879475	0.83[EUR][1000 genomes]
rs16879490	0.83[EUR][1000 genomes]
rs16879507	0.83[EUR][1000 genomes]
rs16879510	0.83[EUR][1000 genomes]
rs16879528	0.83[EUR][1000 genomes]
rs16879532	0.83[EUR][1000 genomes]
rs17454834	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17455002	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17504209	0.83[EUR][1000 genomes]
rs17504475	0.83[EUR][1000 genomes]
rs17504517	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2273131	0.83[EUR][1000 genomes]
rs2307383	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2307389	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2307393	0.84[EUR][1000 genomes]
rs28360511	0.83[EUR][1000 genomes]
rs28381452	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28381487	0.84[EUR][1000 genomes]
rs28381518	0.84[EUR][1000 genomes]
rs28381552	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28385570	0.83[EUR][1000 genomes]
rs28385591	0.84[EUR][1000 genomes]
rs28385632	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34007246	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34008333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34054261	0.83[EUR][1000 genomes]
rs34107692	0.83[EUR][1000 genomes]
rs34154420	0.84[EUR][1000 genomes]
rs34385811	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34395299	0.83[EUR][1000 genomes]
rs34423353	0.84[EUR][1000 genomes]
rs34455158	0.84[EUR][1000 genomes]
rs34540725	0.83[EUR][1000 genomes]
rs34547532	0.83[EUR][1000 genomes]
rs34650015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34727395	0.83[EUR][1000 genomes]
rs34926624	0.90[AMR][1000 genomes]
rs34941612	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35031351	0.83[EUR][1000 genomes]
rs35056836	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35058527	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs35116392	0.83[EUR][1000 genomes]
rs35145047	0.84[EUR][1000 genomes]
rs35237504	0.83[EUR][1000 genomes]
rs35289945	0.83[EUR][1000 genomes]
rs35303040	0.83[EUR][1000 genomes]
rs35317752	0.83[EUR][1000 genomes]
rs35324020	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35350424	0.83[EUR][1000 genomes]
rs35363104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35396056	0.83[EUR][1000 genomes]
rs35440627	1.00[AFR][1000 genomes]
rs35465301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35494431	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35504787	0.83[EUR][1000 genomes]
rs35593940	0.83[EUR][1000 genomes]
rs35607770	1.00[AFR][1000 genomes]
rs35610797	0.83[EUR][1000 genomes]
rs35679038	0.83[EUR][1000 genomes]
rs35866706	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs35903880	0.83[EUR][1000 genomes]
rs35917348	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35925514	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35946241	0.84[EUR][1000 genomes]
rs35965137	1.00[AFR][1000 genomes]
rs35972482	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36020402	0.84[EUR][1000 genomes]
rs36041712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36090981	0.84[EUR][1000 genomes]
rs3734908	0.83[EUR][1000 genomes]
rs3757369	0.83[EUR][1000 genomes]
rs3757371	0.83[EUR][1000 genomes]
rs3763176	1.00[AFR][1000 genomes]
rs4409162	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4587137	0.83[EUR][1000 genomes]
rs55686846	1.00[AFR][1000 genomes]
rs55751639	0.83[EUR][1000 genomes]
rs55759644	0.84[EUR][1000 genomes]
rs55765303	0.83[EUR][1000 genomes]
rs55880748	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56031077	0.84[EUR][1000 genomes]
rs57526195	0.84[EUR][1000 genomes]
rs60313720	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61432898	1.00[AFR][1000 genomes]
rs62417663	0.83[EUR][1000 genomes]
rs62417666	0.83[EUR][1000 genomes]
rs62417673	0.83[EUR][1000 genomes]
rs62417674	0.83[EUR][1000 genomes]
rs62417675	0.83[EUR][1000 genomes]
rs62417676	0.83[EUR][1000 genomes]
rs62417686	0.83[EUR][1000 genomes]
rs62417689	0.80[EUR][1000 genomes]
rs62417692	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62417693	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62417699	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62417700	1.00[AFR][1000 genomes]
rs62417701	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62417715	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62417720	0.84[EUR][1000 genomes]
rs62417727	0.84[EUR][1000 genomes]
rs62417753	1.00[AFR][1000 genomes]
rs62417757	1.00[AFR][1000 genomes]
rs62419368	1.00[AFR][1000 genomes]
rs62419377	1.00[AFR][1000 genomes]
rs62419386	0.83[EUR][1000 genomes]
rs6900057	0.83[EUR][1000 genomes]
rs6902069	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6905345	0.83[EUR][1000 genomes]
rs6905480	0.83[EUR][1000 genomes]
rs6911548	0.83[EUR][1000 genomes]
rs6926321	0.83[EUR][1000 genomes]
rs6927654	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6927826	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6929542	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6940675	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71548716	0.83[EUR][1000 genomes]
rs7738268	0.83[EUR][1000 genomes]
rs7739772	0.83[EUR][1000 genomes]
rs7740476	0.83[EUR][1000 genomes]
rs7741170	0.83[EUR][1000 genomes]
rs7742607	0.83[EUR][1000 genomes]
rs7744190	0.83[EUR][1000 genomes]
rs7749032	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7750528	0.84[EUR][1000 genomes]
rs7750775	0.83[EUR][1000 genomes]
rs7750877	0.80[EUR][1000 genomes]
rs7754550	0.80[EUR][1000 genomes]
rs7757446	0.83[EUR][1000 genomes]
rs7759422	0.84[EUR][1000 genomes]
rs7759648	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7760919	0.83[EUR][1000 genomes]
rs7770458	0.83[EUR][1000 genomes]
rs7771832	0.84[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	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv538354	chr6:88273858-88311606	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88297800-88301400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr6:88298000-88301400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:88298000-88301400	Active TSS	A549	lung
4	chr6:88298800-88301400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:88299000-88301400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:88300400-88302000	Flanking Active TSS	Dnd41	blood
7	chr6:88300400-88320800	Weak transcription	Spleen	Spleen
8	chr6:88300400-88323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:88300600-88301400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:88300600-88301400	Transcr. at gene 5' and 3'	K562	blood
11	chr6:88300600-88301800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:88300600-88302000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:88300600-88302800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:88300600-88315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:88300600-88320000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:88300600-88321800	Weak transcription	Lung	lung
17	chr6:88300600-88323400	Weak transcription	Gastric	stomach
18	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
19	chr6:88300800-88301400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:88300800-88301400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr6:88300800-88301600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr6:88300800-88302000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:88300800-88302400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr6:88300800-88304200	Weak transcription	Placenta	Placenta
25	chr6:88300800-88304200	Weak transcription	Left Ventricle	heart
26	chr6:88300800-88304800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:88300800-88311600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:88300800-88320600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:88300800-88323600	Weak transcription	Aorta	Aorta
30	chr6:88301000-88301400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:88301000-88301400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:88301000-88301400	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr6:88301000-88301400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr6:88301000-88301400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:88301000-88301400	Enhancers	Liver	Liver
36	chr6:88301000-88301400	Enhancers	Brain Hippocampus Middle	brain
37	chr6:88301000-88301400	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr6:88301000-88301400	Enhancers	Duodenum Mucosa	Duodenum
39	chr6:88301000-88301400	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr6:88301000-88301400	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr6:88301000-88301600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr6:88301000-88301600	Enhancers	Ovary	ovary
43	chr6:88301000-88301800	Weak transcription	Fetal Heart	heart
44	chr6:88301000-88301800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr6:88301000-88302000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr6:88301000-88302000	Enhancers	Brain Cingulate Gyrus	brain
47	chr6:88301000-88302400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr6:88301000-88302400	Weak transcription	Fetal Thymus	thymus
49	chr6:88301000-88302600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr6:88301000-88302800	Weak transcription	Fetal Intestine Large	intestine

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