Variant report

Variant	rs16829753
Chromosome Location	chr1:196275125-196275126
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]
rs10922057	1.00[ASN][1000 genomes]
rs16839668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16839682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16839685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16839693	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16839698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16839700	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16839716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16839751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16839758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16839763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16839771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16839782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16839791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16839795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16839822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16839832	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16839841	0.80[EUR][1000 genomes]
rs16839848	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839856	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839872	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839878	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839881	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839884	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839886	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839905	0.90[AMR][1000 genomes]
rs16839906	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839910	1.00[AFR][1000 genomes]
rs16839919	1.00[AFR][1000 genomes]
rs17639647	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2296269	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41451950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74133631	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74133640	0.94[EUR][1000 genomes]
rs74133658	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544202	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7544383	1.00[AFR][1000 genomes];0.90[AMR][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	nsv872952	chr1:196174790-196304223	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv548741	chr1:196186750-196293493	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv832237	chr1:196205674-196328500	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv469680	chr1:196259846-196419016	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv482746	chr1:196259846-196419016	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196249200-196281400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:196256600-196302800	Weak transcription	Ovary	ovary
3	chr1:196266200-196309600	Weak transcription	Fetal Kidney	kidney
4	chr1:196266800-196284400	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:196268800-196304400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:196271400-196276600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:196271600-196276800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr1:196271600-196277000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr1:196272400-196277400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr1:196272600-196275200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:196273000-196313400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:196273200-196275200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:196273400-196282000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:196273400-196284400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:196273800-196281600	Weak transcription	Liver	Liver
16	chr1:196274200-196275400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:196274600-196275400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:196274600-196275400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:196274600-196276600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:196274600-196276800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:196274800-196275200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:196275000-196276600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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