Variant report

Variant	rs7589617
Chromosome Location	chr2:98999373-98999374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10172661	1.00[AMR][1000 genomes]
rs13395005	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13429817	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17030716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17502330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271041	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3754895	0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs3769720	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3769746	0.89[AFR][1000 genomes]
rs3769747	0.90[YRI][hapmap];0.89[AFR][1000 genomes]
rs3769748	0.86[AFR][1000 genomes]
rs6743554	0.85[YRI][hapmap]
rs7562788	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7564438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7604711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1008645	chr2:98915767-99010743	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1013617	chr2:98943377-99004173	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1006328	chr2:98977192-99210376	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98990600-99007200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:98993800-99001000	Weak transcription	Brain Germinal Matrix	brain
3	chr2:98994600-98999400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:98995600-99001000	Weak transcription	Brain Angular Gyrus	brain
5	chr2:98996000-99001400	Weak transcription	Right Atrium	heart
6	chr2:98996800-99003000	Weak transcription	Fetal Brain Female	brain
7	chr2:98997200-98999600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:98997400-98999400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:98997600-99001200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:98998400-99000400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:98999200-98999400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:98999200-98999400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr2:98999200-98999600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
14	chr2:98999200-98999800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr2:98999200-99000200	Enhancers	HUES64 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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