Variant report

Variant	rs62388754
Chromosome Location	chr6:30001703-30001704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29999651..30002590-chr6:30017205..30019223,2	K562	blood:
2	chr6:30001672..30004034-chr6:30026395..30027961,2	K562	blood:

Variant related genes	Relation type
ENSG00000204623	Chromatin interaction
ENSG00000066379	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10484549	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16896044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896851	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16896923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17179992	1.00[AFR][1000 genomes]
rs17180093	1.00[AFR][1000 genomes]
rs17180107	1.00[AFR][1000 genomes]
rs17180227	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17180836	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17186566	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17187693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17193696	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17194467	1.00[AFR][1000 genomes]
rs2275854	0.84[ASN][1000 genomes]
rs2286404	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394249	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2893999	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34823152	1.00[AFR][1000 genomes]
rs3823368	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3869062	1.00[AFR][1000 genomes]
rs41540614	1.00[AFR][1000 genomes]
rs41545022	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs41545117	1.00[AFR][1000 genomes]
rs41547618	1.00[AFR][1000 genomes]
rs41562213	1.00[AFR][1000 genomes]
rs55664658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55808509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55897388	1.00[AFR][1000 genomes]
rs55975201	1.00[AFR][1000 genomes]
rs56052321	1.00[AFR][1000 genomes]
rs56073777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149225	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56171155	1.00[AFR][1000 genomes]
rs56181708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56185319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56232426	1.00[AFR][1000 genomes]
rs56270681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56289102	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56369124	1.00[AFR][1000 genomes]
rs56378970	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58161072	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388660	1.00[AFR][1000 genomes]
rs62388661	1.00[AFR][1000 genomes]
rs62388723	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62388749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390510	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62390517	1.00[AFR][1000 genomes]
rs62390553	1.00[AFR][1000 genomes]
rs62390555	1.00[AFR][1000 genomes]
rs62392214	1.00[AFR][1000 genomes]
rs62392216	1.00[AFR][1000 genomes]
rs7453937	1.00[AFR][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	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv884045	chr6:29997312-30015905	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv884046	chr6:29997312-30023868	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv884047	chr6:29998872-30007493	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29974800-30002400	Weak transcription	Dnd41	blood
2	chr6:29975200-30027800	Weak transcription	Aorta	Aorta
3	chr6:29975600-30027800	Weak transcription	Right Ventricle	heart
4	chr6:29975800-30027800	Weak transcription	Gastric	stomach
5	chr6:29976200-30001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:29976600-30023000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:29977000-30002000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:29977000-30002000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:29977200-30003800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:29977200-30024600	Weak transcription	Brain Anterior Caudate	brain
11	chr6:29977200-30027600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:29977200-30027800	Weak transcription	Fetal Intestine Small	intestine
13	chr6:29979000-30027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:29979400-30024600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:29979600-30022800	Weak transcription	Ovary	ovary
16	chr6:29979800-30027800	Weak transcription	Pancreas	Pancrea
17	chr6:29980200-30012000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:29981200-30023000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:29981800-30010600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:29982800-30009800	Weak transcription	Psoas Muscle	Psoas
21	chr6:29982800-30022800	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:29983400-30012400	Weak transcription	NHEK	skin
23	chr6:29984600-30023400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:29985000-30024600	Weak transcription	Brain Angular Gyrus	brain
25	chr6:29985400-30008200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:29987800-30010600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:29987800-30024800	Weak transcription	Fetal Intestine Large	intestine
28	chr6:29988000-30010400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr6:29988200-30009800	Weak transcription	HepG2	liver
30	chr6:29988200-30022800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:29988200-30027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:29988200-30027800	Weak transcription	Esophagus	oesophagus
33	chr6:29988400-30006200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:29988400-30021600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:29988400-30023400	Weak transcription	Adipose Nuclei	Adipose
36	chr6:29988400-30027800	Weak transcription	Thymus	Thymus
37	chr6:29988600-30003800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:29988600-30009800	Weak transcription	Left Ventricle	heart
39	chr6:29988600-30022200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:29988600-30027400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:29988800-30001800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr6:29988800-30001800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:29988800-30022800	Weak transcription	Brain Hippocampus Middle	brain
44	chr6:29989000-30002400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:29989000-30009800	Weak transcription	GM12878-XiMat	blood
46	chr6:29989000-30023000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:29989400-30021400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr6:29989600-30002400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr6:29989800-30003600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:29996600-30012200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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