Variant report

Variant	rs7571001
Chromosome Location	chr2:98949400-98949401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10172281	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10181000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10190679	0.98[ASN][1000 genomes]
rs10199476	0.87[CHB][hapmap]
rs10210685	0.98[ASN][1000 genomes]
rs11124096	0.87[CHB][hapmap]
rs11124107	0.87[CHB][hapmap]
rs11673807	0.87[CHB][hapmap]
rs11679920	0.87[CHB][hapmap]
rs11889349	0.87[CHB][hapmap]
rs11895654	0.87[CHB][hapmap]
rs12478763	0.87[CHB][hapmap]
rs12622324	0.87[CHB][hapmap]
rs12999985	0.87[CHB][hapmap]
rs13014142	0.87[CHB][hapmap]
rs13394706	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13408372	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13427344	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13428221	0.91[ASN][1000 genomes]
rs13432099	0.98[ASN][1000 genomes]
rs1451251	0.93[CHB][hapmap]
rs1466944	0.87[ASW][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs1546351	0.84[YRI][hapmap]
rs17429208	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2055591	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2102270	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs2122756	0.87[CHB][hapmap]
rs2202387	0.87[CHB][hapmap]
rs2221416	0.87[CHB][hapmap]
rs2292118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2292119	0.87[CHB][hapmap];0.95[YRI][hapmap]
rs3769755	0.80[CHB][hapmap]
rs4374424	0.87[CHB][hapmap]
rs4455212	0.92[CHB][hapmap]
rs4477970	0.87[CHB][hapmap]
rs4479470	0.87[CHB][hapmap]
rs4608580	0.87[CHB][hapmap]
rs4632400	0.87[CHB][hapmap]
rs4851124	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4851935	0.87[CHB][hapmap]
rs4851951	0.92[CHB][hapmap]
rs56320609	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60924437	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs62156263	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs62156264	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6543419	0.87[CHB][hapmap]
rs6715989	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6725543	0.87[CHB][hapmap];0.81[MEX][hapmap]
rs6742930	0.89[AFR][1000 genomes]
rs6747344	0.87[CHB][hapmap]
rs6747410	1.00[CHB][hapmap]
rs6754222	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72819909	0.98[ASN][1000 genomes]
rs7571110	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7578802	0.87[CHB][hapmap]
rs7580008	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586663	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7601049	0.87[CHB][hapmap]
rs7606220	0.87[CHB][hapmap]

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	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	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	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
5	nsv1010466	chr2:98938886-98998109	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7571001	ANKRD39	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98940600-98949400	Weak transcription	Osteobl	bone
2	chr2:98946800-98950400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:98948400-98951400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:98948800-98952800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr2:98949000-98950200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:98949000-98953200	Enhancers	Brain Germinal Matrix	brain
7	chr2:98949200-98950000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:98949200-98950000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:98949200-98950800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:98949200-98952000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:98949400-98950000	Enhancers	Osteobl	bone
12	chr2:98949400-98950600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:98949400-98951200	Enhancers	NHDF-Ad	bronchial
14	chr2:98949400-98951600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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