Variant report

Variant	rs9301926
Chromosome Location	chr13:94681840-94681841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10492635	1.00[CEU][hapmap]
rs1318496	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1415736	0.91[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.89[TSI][hapmap]
rs1415737	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.96[TSI][hapmap];1.00[EUR][1000 genomes]
rs1415743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556082	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs17253537	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[EUR][1000 genomes]
rs1933146	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs1933147	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs2021983	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6492685	0.91[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.89[TSI][hapmap]
rs6650320	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs6650321	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs72644500	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7323264	0.82[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.80[TSI][hapmap]
rs7325794	0.82[CEU][hapmap]
rs7985851	0.82[CEU][hapmap]
rs7994682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs928188	0.82[YRI][hapmap]
rs9284275	0.89[CHB][hapmap];0.88[CHD][hapmap]
rs9284276	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs9301920	0.82[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap]
rs9301921	0.82[CEU][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs9516319	0.89[CHB][hapmap];0.88[CHD][hapmap]
rs9516322	0.80[EUR][1000 genomes]
rs9516323	0.89[CHB][hapmap];0.90[CHD][hapmap]
rs9516324	0.88[CHB][hapmap]
rs9516330	0.88[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9516331	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9516332	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9524284	0.82[CEU][hapmap]
rs9524290	0.89[CHB][hapmap];0.90[CHD][hapmap]
rs9524292	0.82[CEU][hapmap]
rs9524300	0.82[CHB][hapmap]
rs9524302	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9524304	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9524305	0.91[CEU][hapmap]
rs9524306	1.00[CEU][hapmap]
rs9524309	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9524310	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9524311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524312	1.00[CEU][hapmap];0.89[CHB][hapmap];0.98[EUR][1000 genomes]
rs9524313	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524315	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9524316	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[EUR][1000 genomes]
rs9524317	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs9524318	1.00[CEU][hapmap];0.93[CHB][hapmap]
rs9524319	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap]
rs9561490	0.91[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap]
rs9561491	0.91[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap]
rs9584176	0.88[CHB][hapmap]
rs9584177	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9584178	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9589877	0.89[CHB][hapmap];0.90[CHD][hapmap]
rs9589878	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9589880	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9589881	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9589882	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9589883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9589884	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948714	chr13:94100104-94699435	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv933807	chr13:94187158-94845505	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1045230	chr13:94277683-94764671	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv948455	chr13:94451368-94988900	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv916640	chr13:94521959-95101443	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv533063	chr13:94560362-95101443	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1052141	chr13:94596760-94689892	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv900923	chr13:94641894-94692925	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9301926	CCL23	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94675000-94683400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:94678600-94686400	Weak transcription	Fetal Stomach	stomach
3	chr13:94680000-94682000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr13:94680400-94682000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr13:94681200-94683200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:94681200-94683200	Weak transcription	Ovary	ovary
7	chr13:94681200-94683600	Weak transcription	Fetal Intestine Large	intestine
8	chr13:94681200-94685200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr13:94681400-94683200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr13:94681600-94682800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:94681600-94682800	Weak transcription	Colon Smooth Muscle	Colon
12	chr13:94681600-94682800	Weak transcription	Fetal Heart	heart
13	chr13:94681600-94685600	Weak transcription	Brain Germinal Matrix	brain
14	chr13:94681600-94685800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr13:94681800-94682000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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