Variant report

Variant	rs2576238
Chromosome Location	chr1:216983409-216983410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1030846	0.88[CEU][hapmap];0.91[CHD][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1126022	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1339337	0.88[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1339338	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339348	0.83[CEU][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1339356	0.84[CEU][hapmap];0.91[CHD][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1344873	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1436888	0.83[EUR][1000 genomes]
rs1538526	0.89[JPT][hapmap]
rs1832532	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2032028	0.84[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2118151	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2576231	0.89[JPT][hapmap]
rs2576234	0.84[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2576235	0.84[ASW][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2576236	0.84[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2789716	0.88[CEU][hapmap];0.91[CHD][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2789720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2813671	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2813674	0.82[CEU][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4575149	0.96[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6604647	0.84[CEU][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7512365	0.96[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7554036	0.83[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][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	esv2762163	chr1:216982140-217015625	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
2	esv3430243	chr1:216983179-216985177	Enhancers Weak transcription Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2576238	C1orf97	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216979000-216986200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:216979800-216985000	Weak transcription	Fetal Heart	heart
3	chr1:216979800-216985200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:216979800-216988800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:216979800-216989000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:216980000-216984800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:216980200-216986400	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:216980200-216987400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:216980400-216988000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:216981200-216986000	Weak transcription	HSMMtube	muscle
11	chr1:216983000-216983600	Enhancers	Psoas Muscle	Psoas
12	chr1:216983200-216983600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:216983200-216988600	Weak transcription	Right Atrium	heart
14	chr1:216983200-216989200	Weak transcription	Gastric	stomach
15	chr1:216983400-216983600	Enhancers	Left Ventricle	heart

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