Variant report

Variant	rs6680668
Chromosome Location	chr1:180357171-180357172
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10914021	0.81[EUR][1000 genomes]
rs13373944	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13374104	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13374665	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13376342	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1416822	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17300282	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17300340	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17300600	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17300712	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17372281	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17372295	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17372362	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17372667	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28816398	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4405110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4446932	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4651065	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56759227	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57537558	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57882351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58047798	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58677059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59022209	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59113753	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59829460	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60927564	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6425643	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6672501	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6694896	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6702245	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6704001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72712995	0.91[EUR][1000 genomes]
rs72713000	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72714804	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72714834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714855	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714861	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714864	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714866	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714870	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714877	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714879	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714887	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714902	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72716607	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72716615	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72716616	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72716625	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72716627	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72716629	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72716632	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72720914	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74132851	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs74135185	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7517775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7525689	0.80[EUR][1000 genomes]
rs946636	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs961162	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9650999	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
8	nsv1009742	chr1:180342203-180385459	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180341200-180401400	Weak transcription	Osteobl	bone
2	chr1:180348200-180382600	Weak transcription	Pancreas	Pancrea
3	chr1:180349400-180364200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:180349400-180407000	Weak transcription	Esophagus	oesophagus
5	chr1:180351600-180378400	Weak transcription	HSMM	muscle
6	chr1:180352400-180381400	Weak transcription	Hela-S3	cervix
7	chr1:180352800-180399400	Weak transcription	Fetal Thymus	thymus
8	chr1:180354200-180364200	Weak transcription	NH-A	brain
9	chr1:180354600-180374000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:180354800-180358600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:180354800-180386600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:180355000-180360600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:180355200-180364800	Weak transcription	K562	blood
14	chr1:180355200-180402600	Weak transcription	HMEC	breast
15	chr1:180355400-180361200	Weak transcription	Small Intestine	intestine
16	chr1:180355400-180378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:180355600-180378400	Weak transcription	Placenta	Placenta
18	chr1:180355600-180390800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:180356400-180363800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:180356600-180364200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:180356600-180364200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:180356600-180381400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:180356600-180394000	Weak transcription	NHDF-Ad	bronchial
24	chr1:180356800-180363600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:180356800-180364200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:180356800-180364800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:180356800-180373000	Weak transcription	Fetal Intestine Small	intestine
28	chr1:180356800-180378600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:180356800-180378800	Weak transcription	Left Ventricle	heart
30	chr1:180356800-180380800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:180356800-180406200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:180356800-180407000	Weak transcription	Aorta	Aorta
33	chr1:180357000-180357600	Enhancers	GM12878-XiMat	blood
34	chr1:180357000-180358800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:180357000-180359800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:180357000-180359800	Weak transcription	Primary B cells from cord blood	blood
37	chr1:180357000-180359800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:180357000-180359800	Weak transcription	A549	lung
39	chr1:180357000-180360000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:180357000-180360600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr1:180357000-180360600	Weak transcription	Dnd41	blood
42	chr1:180357000-180361200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:180357000-180364000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:180357000-180364200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:180357000-180364200	Weak transcription	Fetal Intestine Large	intestine
46	chr1:180357000-180364200	Weak transcription	Ovary	ovary
47	chr1:180357000-180364400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:180357000-180378400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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