Variant report

Variant	rs199678
Chromosome Location	chr1:77487891-77487892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1502524	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs199677	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199679	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199680	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199681	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199683	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199685	0.88[CEU][hapmap];0.94[CHD][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs199686	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs199687	0.88[CHD][hapmap]
rs199688	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs199689	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199690	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199692	1.00[ASN][1000 genomes]
rs199693	0.98[ASN][1000 genomes]
rs199694	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2350525	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384473	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434497	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451650	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613378	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv830292	chr1:77425571-77584307	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77477000-77491400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:77478000-77489000	Weak transcription	Fetal Stomach	stomach
3	chr1:77484800-77492000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:77485200-77489000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:77485200-77490200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:77485200-77490200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:77485200-77493000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:77485200-77494800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:77485200-77495200	Weak transcription	Ovary	ovary
10	chr1:77485600-77488800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:77485600-77491400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:77485600-77491800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:77486000-77491600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:77486000-77491800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:77486200-77490200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:77486200-77495800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:77486200-77496600	Weak transcription	NHEK	skin
18	chr1:77486400-77488000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:77486400-77490600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:77486600-77491400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:77486800-77488000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:77486800-77492000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:77487200-77488400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr1:77487200-77491400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:77487800-77490400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:77487800-77491800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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