Variant report

Variant	rs62417757
Chromosome Location	chr6:88399567-88399568
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88397239..88400435-chr6:88400607..88403655,3	K562	blood:
2	chr6:88392656..88394739-chr6:88399479..88401208,2	K562	blood:
3	chr6:88397600..88401322-chr6:88403736..88407504,4	K562	blood:
4	chr6:88399461..88401645-chr6:88409406..88411784,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 161 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs12190021	1.00[ASN][1000 genomes]
rs12203759	1.00[ASN][1000 genomes]
rs13193193	1.00[AFR][1000 genomes]
rs13193303	0.81[EUR][1000 genomes]
rs13193470	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13193703	0.81[EUR][1000 genomes]
rs13193927	0.81[EUR][1000 genomes]
rs13196538	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13196755	0.81[EUR][1000 genomes]
rs13197090	0.81[EUR][1000 genomes]
rs13198094	0.81[EUR][1000 genomes]
rs13200106	0.81[EUR][1000 genomes]
rs13202825	0.81[EUR][1000 genomes]
rs13203056	0.81[EUR][1000 genomes]
rs13203649	0.81[EUR][1000 genomes]
rs13203957	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13204592	0.81[EUR][1000 genomes]
rs13204861	0.81[EUR][1000 genomes]
rs13206536	0.81[EUR][1000 genomes]
rs13206957	0.81[EUR][1000 genomes]
rs13208201	1.00[AFR][1000 genomes]
rs13208550	0.81[EUR][1000 genomes]
rs13208933	0.81[EUR][1000 genomes]
rs13210643	0.81[EUR][1000 genomes]
rs13211439	0.81[EUR][1000 genomes]
rs13211833	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13212076	0.81[EUR][1000 genomes]
rs13212089	0.81[EUR][1000 genomes]
rs13213285	0.81[EUR][1000 genomes]
rs13215013	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13215887	0.81[EUR][1000 genomes]
rs13216482	1.00[AFR][1000 genomes]
rs13216724	0.81[EUR][1000 genomes]
rs13216727	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13219631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16879475	0.81[EUR][1000 genomes]
rs16879490	0.81[EUR][1000 genomes]
rs16879507	0.81[EUR][1000 genomes]
rs16879510	0.81[EUR][1000 genomes]
rs16879528	0.81[EUR][1000 genomes]
rs16879532	0.81[EUR][1000 genomes]
rs17454834	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17455002	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17504209	0.81[EUR][1000 genomes]
rs17504475	0.81[EUR][1000 genomes]
rs17504517	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2273131	0.81[EUR][1000 genomes]
rs2307383	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2307389	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2307393	0.87[EUR][1000 genomes]
rs28360511	0.81[EUR][1000 genomes]
rs28381487	0.81[EUR][1000 genomes]
rs28381518	0.87[EUR][1000 genomes]
rs28381552	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs28385570	0.81[EUR][1000 genomes]
rs28385591	0.81[EUR][1000 genomes]
rs28752032	1.00[ASN][1000 genomes]
rs34007246	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34008333	1.00[AFR][1000 genomes]
rs34054261	0.81[EUR][1000 genomes]
rs34080809	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34107692	0.81[EUR][1000 genomes]
rs34154420	0.81[EUR][1000 genomes]
rs34395299	0.81[EUR][1000 genomes]
rs34423353	0.87[EUR][1000 genomes]
rs34455158	0.81[EUR][1000 genomes]
rs34540725	0.81[EUR][1000 genomes]
rs34547532	0.81[EUR][1000 genomes]
rs34650015	1.00[AFR][1000 genomes]
rs34727395	0.81[EUR][1000 genomes]
rs34941612	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35031351	0.81[EUR][1000 genomes]
rs35056836	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35058527	1.00[AFR][1000 genomes]
rs35116392	0.81[EUR][1000 genomes]
rs35145047	0.87[EUR][1000 genomes]
rs35237504	0.81[EUR][1000 genomes]
rs35289945	0.81[EUR][1000 genomes]
rs35303040	0.81[EUR][1000 genomes]
rs35317752	0.81[EUR][1000 genomes]
rs35324020	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35326820	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35350424	0.81[EUR][1000 genomes]
rs35363104	1.00[AFR][1000 genomes]
rs35396056	0.81[EUR][1000 genomes]
rs35440627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35465301	1.00[AFR][1000 genomes]
rs35494431	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35504787	0.81[EUR][1000 genomes]
rs35593940	0.81[EUR][1000 genomes]
rs35607770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35610797	0.81[EUR][1000 genomes]
rs35679038	0.81[EUR][1000 genomes]
rs35866706	1.00[AFR][1000 genomes]
rs35903880	0.81[EUR][1000 genomes]
rs35917348	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35925514	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35946241	0.87[EUR][1000 genomes]
rs35965137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36020402	0.81[EUR][1000 genomes]
rs36041712	1.00[AFR][1000 genomes]
rs36090981	0.87[EUR][1000 genomes]
rs3734908	0.81[EUR][1000 genomes]
rs3757369	0.81[EUR][1000 genomes]
rs3757371	0.81[EUR][1000 genomes]
rs3763176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4409162	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4587137	0.81[EUR][1000 genomes]
rs55686846	1.00[AFR][1000 genomes]
rs55751639	0.81[EUR][1000 genomes]
rs55759644	0.81[EUR][1000 genomes]
rs55765303	0.81[EUR][1000 genomes]
rs55880748	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56031077	0.81[EUR][1000 genomes]
rs57526195	0.87[EUR][1000 genomes]
rs60313720	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61432898	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62417663	0.81[EUR][1000 genomes]
rs62417666	0.81[EUR][1000 genomes]
rs62417673	0.81[EUR][1000 genomes]
rs62417674	0.81[EUR][1000 genomes]
rs62417675	0.81[EUR][1000 genomes]
rs62417676	0.81[EUR][1000 genomes]
rs62417686	0.81[EUR][1000 genomes]
rs62417692	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62417693	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62417698	1.00[AFR][1000 genomes]
rs62417700	1.00[AFR][1000 genomes]
rs62417715	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62417720	0.81[EUR][1000 genomes]
rs62417727	0.87[EUR][1000 genomes]
rs62417753	1.00[AFR][1000 genomes]
rs62419377	1.00[AFR][1000 genomes]
rs62419386	0.81[EUR][1000 genomes]
rs62419465	0.89[ASN][1000 genomes]
rs62419466	0.89[ASN][1000 genomes]
rs6900057	0.81[EUR][1000 genomes]
rs6905345	0.81[EUR][1000 genomes]
rs6905480	0.81[EUR][1000 genomes]
rs6911548	0.81[EUR][1000 genomes]
rs6926321	0.81[EUR][1000 genomes]
rs71548716	0.81[EUR][1000 genomes]
rs7738268	0.81[EUR][1000 genomes]
rs7739772	0.81[EUR][1000 genomes]
rs7740476	0.81[EUR][1000 genomes]
rs7741170	0.81[EUR][1000 genomes]
rs7742607	0.81[EUR][1000 genomes]
rs7744190	0.81[EUR][1000 genomes]
rs7749032	0.81[EUR][1000 genomes]
rs7750528	0.81[EUR][1000 genomes]
rs7750775	0.81[EUR][1000 genomes]
rs7757446	0.81[EUR][1000 genomes]
rs7759422	0.81[EUR][1000 genomes]
rs7760919	0.81[EUR][1000 genomes]
rs7770458	0.81[EUR][1000 genomes]
rs7771832	0.81[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	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
2	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
3	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
4	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:88381400-88400600	Weak transcription	Right Atrium	heart
4	chr6:88385400-88399800	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:88385400-88401200	Weak transcription	Fetal Heart	heart
6	chr6:88387600-88407000	Weak transcription	Fetal Kidney	kidney
7	chr6:88387800-88400600	Weak transcription	K562	blood
8	chr6:88388000-88401400	Weak transcription	Placenta	Placenta
9	chr6:88388000-88410400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:88389200-88406800	Weak transcription	Fetal Stomach	stomach
11	chr6:88389600-88401400	Weak transcription	Fetal Brain Female	brain
12	chr6:88390200-88401200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr6:88390400-88399600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:88390400-88400400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:88390400-88400800	Weak transcription	Pancreas	Pancrea
16	chr6:88390400-88401200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:88390400-88401400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:88390400-88401800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:88390400-88405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:88390400-88410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:88391000-88405200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:88391200-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:88391400-88400800	Weak transcription	Brain Germinal Matrix	brain
24	chr6:88391400-88400800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:88391800-88399600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:88392000-88400000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:88392000-88401200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:88392200-88400000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:88392200-88405200	Weak transcription	Fetal Brain Male	brain
30	chr6:88392400-88400600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:88392400-88400800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:88392400-88401400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr6:88392400-88407200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:88392400-88407400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:88392400-88407400	Weak transcription	Aorta	Aorta
36	chr6:88392600-88399800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:88392600-88406800	Weak transcription	HSMM	muscle
38	chr6:88392600-88407200	Weak transcription	HMEC	breast
39	chr6:88393000-88400000	Weak transcription	Osteobl	bone
40	chr6:88393000-88401200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:88393000-88401400	Weak transcription	NHEK	skin
42	chr6:88393600-88402600	Weak transcription	Esophagus	oesophagus
43	chr6:88393600-88404000	Weak transcription	HUVEC	blood vessel
44	chr6:88393800-88405600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:88394000-88401200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:88394200-88399600	Enhancers	Liver	Liver
47	chr6:88394600-88401400	Weak transcription	Primary T cells from cord blood	blood
48	chr6:88394800-88402200	Enhancers	Adipose Nuclei	Adipose
49	chr6:88395000-88407200	Weak transcription	Hela-S3	cervix
50	chr6:88395200-88400600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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