Variant report

Variant	rs1416962
Chromosome Location	chr1:196454628-196454629
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:196448595..196456381-chr1:196458214..196462920,9	K562	blood:
2	chr1:196448856..196453298-chr1:196454594..196458706,6	K562	blood:
3	chr1:196440873..196444078-chr1:196452789..196457047,3	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10494743	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10737670	0.90[JPT][hapmap]
rs10754187	0.90[JPT][hapmap]
rs10754188	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10754195	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs10754196	0.84[JPT][hapmap]
rs10801530	0.90[JPT][hapmap]
rs10801531	0.90[JPT][hapmap]
rs10801532	0.89[JPT][hapmap]
rs10801533	0.86[CEU][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs10801537	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10801538	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10801539	0.83[ASN][1000 genomes]
rs10922067	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10922068	0.87[EUR][1000 genomes]
rs10922071	0.80[CHB][hapmap];0.81[CHD][hapmap];0.80[ASN][1000 genomes]
rs10922073	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10922075	0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10922078	0.85[ASN][1000 genomes]
rs10922082	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10922083	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10922084	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10922088	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs11576790	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11807331	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12034150	0.86[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs12049567	0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs12065463	0.86[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12065519	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12069983	0.89[JPT][hapmap]
rs12069990	0.89[JPT][hapmap]
rs12121250	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12123128	0.89[ASN][1000 genomes]
rs12562176	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12727032	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12729649	0.90[JPT][hapmap]
rs1538684	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1538686	0.90[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1538687	0.89[JPT][hapmap]
rs16840224	0.84[JPT][hapmap]
rs1769996	0.90[JPT][hapmap]
rs1832617	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2027368	0.89[JPT][hapmap]
rs2878551	0.86[CHD][hapmap]
rs2878557	0.89[JPT][hapmap]
rs2878559	0.86[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs35582782	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3855964	0.89[JPT][hapmap]
rs3927686	0.89[JPT][hapmap]
rs3928857	0.89[JPT][hapmap]
rs4425932	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4462080	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4618911	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4658039	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs60495441	0.87[ASN][1000 genomes]
rs61820915	0.80[ASN][1000 genomes]
rs6428349	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs6696801	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697795	0.84[ASN][1000 genomes]
rs72732257	0.92[ASN][1000 genomes]
rs72732259	0.89[ASN][1000 genomes]
rs7515074	0.95[JPT][hapmap]
rs7515472	0.80[EUR][1000 genomes]
rs7527415	0.95[JPT][hapmap]
rs7531611	0.89[JPT][hapmap]
rs7535696	0.89[JPT][hapmap]
rs7551077	0.80[EUR][1000 genomes]
rs869257	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9427622	0.88[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs946750	0.89[JPT][hapmap]
rs946755	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9659527	0.82[CEU][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1009233	chr1:196301712-196568874	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196420000-196460800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:196434200-196459200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:196434600-196459600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:196436400-196485200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:196437400-196467800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:196447400-196458200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:196447800-196468000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:196448400-196457600	Weak transcription	Fetal Kidney	kidney
9	chr1:196450000-196459800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:196450600-196462200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:196451200-196462200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:196451400-196467600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:196452800-196471200	Weak transcription	Liver	Liver
14	chr1:196454400-196467400	Weak transcription	Ovary	ovary

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