Variant report

Variant	rs6429556
Chromosome Location	chr1:45510660-45510661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45496126..45498745-chr1:45510128..45512403,2	K562	blood:
2	chr1:45505490..45509535-chr1:45509540..45512957,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1152028	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11548990	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1226732	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1226750	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1612575	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs173208	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1969084	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1995403	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2105460	0.87[ASN][1000 genomes]
rs2228084	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2234480	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs346685	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346686	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs346688	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346689	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346692	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346703	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346704	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346709	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346710	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs346711	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346718	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346720	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346725	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346726	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346730	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs409082	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs412055	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs41312020	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4415614	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4660835	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55826381	0.85[ASN][1000 genomes]
rs55842174	0.89[ASN][1000 genomes]
rs55884892	0.85[ASN][1000 genomes]
rs59432881	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61574129	0.87[ASN][1000 genomes]
rs6664113	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6693885	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72684406	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72684412	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72684416	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72684425	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72684426	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72684447	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72684454	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72684481	0.89[ASN][1000 genomes]
rs72684482	0.89[ASN][1000 genomes]
rs72684485	0.89[ASN][1000 genomes]
rs72684487	0.89[ASN][1000 genomes]
rs72684488	0.89[ASN][1000 genomes]
rs72684496	0.81[ASN][1000 genomes]
rs72684499	0.89[ASN][1000 genomes]
rs72686404	0.89[ASN][1000 genomes]
rs7528534	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7543211	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][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	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS 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 target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	nsv546148	chr1:45500294-45627663	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45481200-45525000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:45481200-45527400	Weak transcription	Left Ventricle	heart
3	chr1:45482000-45523800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:45491800-45516400	Weak transcription	Spleen	Spleen
5	chr1:45497400-45525400	Weak transcription	Gastric	stomach
6	chr1:45498000-45525600	Weak transcription	Pancreas	Pancrea
7	chr1:45499200-45516200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:45500400-45516600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:45501400-45516600	Weak transcription	Small Intestine	intestine
10	chr1:45501800-45516200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:45501800-45521200	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:45501800-45527000	Weak transcription	Fetal Brain Male	brain
13	chr1:45502000-45512800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:45502000-45523800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:45502400-45523000	Weak transcription	Aorta	Aorta
16	chr1:45504200-45524200	Weak transcription	Esophagus	oesophagus
17	chr1:45504400-45524000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:45504800-45516400	Weak transcription	Fetal Intestine Large	intestine
19	chr1:45505000-45526000	Weak transcription	Fetal Stomach	stomach
20	chr1:45505200-45514600	Weak transcription	Fetal Intestine Small	intestine
21	chr1:45507600-45527000	Weak transcription	Fetal Kidney	kidney
22	chr1:45508800-45516200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:45509000-45523000	Weak transcription	Brain Angular Gyrus	brain
24	chr1:45509000-45523800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:45509000-45524000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:45509200-45511400	Weak transcription	Ovary	ovary
27	chr1:45509200-45515400	Weak transcription	Brain Substantia Nigra	brain
28	chr1:45509200-45521000	Weak transcription	Brain Anterior Caudate	brain
29	chr1:45509200-45522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:45509400-45511200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:45509400-45512200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:45509400-45513200	Weak transcription	Fetal Brain Female	brain
33	chr1:45509600-45514400	Weak transcription	HepG2	liver
34	chr1:45509600-45516200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:45509600-45516400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:45509600-45522400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:45509600-45526200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:45509800-45511000	Weak transcription	Brain Germinal Matrix	brain
39	chr1:45510000-45516000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:45510600-45511200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:45510600-45511400	Strong transcription	Rectal Mucosa Donor 29	rectum

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