Variant report

Variant	rs2516641
Chromosome Location	chr6:30528685-30528686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30528596-30529667	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr6:30528672-30529516	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr6:30528637-30529591	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr6:30528616-30532626	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30461955..30465538-chr6:30528030..30531365,3	K562	blood:

Variant related genes	Relation type
GNL1	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1058318	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1264432	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1264437	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1264438	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1264439	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1264440	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264448	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1264456	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1362119	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1468079	0.88[EUR][1000 genomes]
rs2023608	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2023609	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2074503	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074504	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074505	0.90[EUR][1000 genomes]
rs2252745	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2269709	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2269710	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2429655	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2429656	0.81[EUR][1000 genomes]
rs2516639	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2516642	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2516643	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2516644	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2516646	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2516648	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2516649	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2516653	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2516656	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2516662	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2524221	0.88[EUR][1000 genomes]
rs2524223	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2524224	0.87[EUR][1000 genomes]
rs2524225	0.83[EUR][1000 genomes]
rs2524226	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2534802	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2534803	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2534804	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2534805	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2534806	0.80[EUR][1000 genomes]
rs2534807	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2534808	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2534809	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2534810	0.86[EUR][1000 genomes]
rs2534812	0.80[EUR][1000 genomes]
rs2534813	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2534814	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2534815	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2534817	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2534820	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2534821	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2534823	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2534824	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2534825	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2844713	0.88[EUR][1000 genomes]
rs2844714	0.88[EUR][1000 genomes]
rs2844715	0.88[EUR][1000 genomes]
rs2844716	0.81[EUR][1000 genomes]
rs2844717	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2844718	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2844720	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2844723	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2844724	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2844725	0.82[EUR][1000 genomes]
rs3094718	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130039	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130041	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3130043	0.85[EUR][1000 genomes]
rs3130045	0.82[EUR][1000 genomes]
rs3130240	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3130242	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130243	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3130244	0.85[EUR][1000 genomes]
rs3132609	0.86[EUR][1000 genomes]
rs3132612	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3132613	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3132614	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9262082	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9262118	0.85[EUR][1000 genomes]
rs975195	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs996588	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs996589	0.82[AMR][1000 genomes];0.87[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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv884091	chr6:30526026-30590646	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	776 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30525600-30529600	Weak transcription	Gastric	stomach
2	chr6:30525800-30529200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:30525800-30529600	Weak transcription	Colonic Mucosa	Colon
4	chr6:30525800-30529600	Weak transcription	Ovary	ovary
5	chr6:30525800-30529800	Weak transcription	Aorta	Aorta
6	chr6:30526000-30528800	Weak transcription	Placenta	Placenta
7	chr6:30526000-30529000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:30526000-30529000	Weak transcription	Left Ventricle	heart
9	chr6:30526000-30529200	Weak transcription	Lung	lung
10	chr6:30526000-30529200	Weak transcription	Right Ventricle	heart
11	chr6:30526000-30529400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:30526000-30529400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:30526000-30529600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:30526000-30529800	Weak transcription	Esophagus	oesophagus
15	chr6:30526000-30530200	Weak transcription	Pancreas	Pancrea
16	chr6:30526000-30530200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:30526000-30530800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:30526000-30537800	Weak transcription	Small Intestine	intestine
19	chr6:30526000-30538400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:30526000-30538600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:30526200-30529000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:30526200-30529000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:30526200-30529000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:30526200-30529200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:30526200-30529200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr6:30526200-30529200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:30526200-30529200	Weak transcription	NH-A	brain
28	chr6:30526200-30529400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:30526200-30529600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:30526200-30529600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:30526200-30529600	Weak transcription	Psoas Muscle	Psoas
32	chr6:30526200-30529800	Weak transcription	Brain Angular Gyrus	brain
33	chr6:30526200-30529800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:30526200-30530200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:30526200-30530200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:30526200-30530200	Weak transcription	HSMMtube	muscle
37	chr6:30526200-30530200	Weak transcription	NHEK	skin
38	chr6:30526200-30530600	Weak transcription	Fetal Kidney	kidney
39	chr6:30526200-30538200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:30526400-30528800	Weak transcription	Primary T cells from cord blood	blood
41	chr6:30526400-30528800	Weak transcription	Fetal Brain Female	brain
42	chr6:30526400-30529000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:30526400-30529000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:30526400-30529000	Weak transcription	Adipose Nuclei	Adipose
45	chr6:30526400-30529000	Weak transcription	Brain Anterior Caudate	brain
46	chr6:30526400-30529000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:30526400-30529000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr6:30526400-30529000	Weak transcription	NHLF	lung
49	chr6:30526400-30529200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:30526400-30529200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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