Variant report

Variant	rs6663802
Chromosome Location	chr1:84875389-84875390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11163955	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11163957	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11163958	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11163959	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11163960	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11163963	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11578928	0.90[CHB][hapmap]
rs12027418	0.85[CEU][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12029581	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12029668	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12030472	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12032962	0.86[ASN][1000 genomes]
rs12034438	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12036961	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12123671	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1246386	0.90[JPT][hapmap]
rs1246392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12740453	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1340595	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1506699	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1506700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1542963	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17131659	0.90[JPT][hapmap]
rs1971350	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1981254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1995643	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2063037	0.86[ASN][1000 genomes]
rs2066197	0.89[ASN][1000 genomes]
rs2104210	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2185486	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389723	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3116415	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3116433	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3116435	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3117747	0.90[JPT][hapmap]
rs3121147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35459071	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768253	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3813608	1.00[JPT][hapmap]
rs3956461	0.90[JPT][hapmap]
rs472601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4907063	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4907064	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4907070	0.87[ASN][1000 genomes]
rs507772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511339	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs528310	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs553775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs601564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6576700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6576701	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6576702	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6576708	0.86[ASN][1000 genomes]
rs676987	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs679725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs925014	0.86[ASN][1000 genomes]
rs937840	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84872000-84876400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:84872400-84876800	Weak transcription	Gastric	stomach
3	chr1:84873200-84876400	Weak transcription	Osteobl	bone
4	chr1:84874000-84876000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:84874000-84876000	Weak transcription	HUVEC	blood vessel
6	chr1:84874000-84878200	Weak transcription	Psoas Muscle	Psoas
7	chr1:84874200-84875400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:84874200-84875600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:84874200-84876200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:84874200-84876400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:84874200-84878000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:84874200-84878200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:84874400-84878200	Weak transcription	Aorta	Aorta
14	chr1:84874800-84876600	Enhancers	Liver	Liver
15	chr1:84874800-84877000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:84874800-84877000	Enhancers	Fetal Intestine Large	intestine
17	chr1:84874800-84877000	Enhancers	Fetal Intestine Small	intestine
18	chr1:84874800-84877000	Enhancers	Stomach Mucosa	stomach
19	chr1:84875000-84876800	Enhancers	Brain Hippocampus Middle	brain
20	chr1:84875200-84875600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:84875200-84875800	Enhancers	Duodenum Mucosa	Duodenum

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