Variant report

Variant	rs6688592
Chromosome Location	chr1:168657541-168657542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10489358	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10489359	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918958	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1108637	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11588432	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588434	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590795	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799741	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11808391	0.81[AFR][1000 genomes]
rs12094644	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12726636	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12727749	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745063	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12748015	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749426	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749876	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337747	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337748	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412334	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412335	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1412336	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1415678	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415680	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16861287	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17502304	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502351	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502574	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561671	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223911	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2419126	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2419128	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34099957	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35492795	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4437856	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58620990	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs726055	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7416358	0.85[AMR][1000 genomes];0.86[EUR][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	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv831836	chr1:168538779-168716956	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872530	chr1:168618641-168658544	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1001684	chr1:168636622-168663398	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv525556	chr1:168653857-168662352	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168653800-168658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:168654800-168657800	Enhancers	HepG2	liver
3	chr1:168655200-168659600	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr1:168656200-168660800	Enhancers	Colon Smooth Muscle	Colon
5	chr1:168656400-168657800	Weak transcription	A549	lung
6	chr1:168656400-168658000	Weak transcription	Fetal Intestine Large	intestine
7	chr1:168656600-168657800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:168656800-168658200	Enhancers	Fetal Kidney	kidney
9	chr1:168657000-168661000	Enhancers	Rectal Smooth Muscle	rectum
10	chr1:168657200-168658000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:168657200-168658000	Weak transcription	Pancreas	Pancrea
12	chr1:168657200-168658800	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr1:168657200-168658800	Enhancers	Stomach Smooth Muscle	stomach
14	chr1:168657200-168659400	Enhancers	Stomach Mucosa	stomach
15	chr1:168657200-168660600	Enhancers	Fetal Heart	heart
16	chr1:168657400-168659400	Enhancers	Duodenum Smooth Muscle	Duodenum

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