Variant report

Variant	rs11709036
Chromosome Location	chr3:142809367-142809368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142805513..142808227-chr3:142808677..142811250,2	K562	blood:
2	chr3:142808907..142811518-chr3:142836983..142839712,2	K562	blood:
3	chr3:142805683..142809398-chr3:142813217..142818159,4	K562	blood:
4	chr3:142752666..142754615-chr3:142809170..142812042,2	K562	blood:

Variant related genes	Relation type
ENSG00000175040	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10413	0.80[EUR][1000 genomes]
rs1043898	0.96[CEU][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs10451867	0.84[EUR][1000 genomes]
rs10513184	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs1053950	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs10790	0.85[CEU][hapmap];0.80[CHB][hapmap];0.80[TSI][hapmap]
rs10935475	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs10935479	0.81[EUR][1000 genomes]
rs12490776	0.84[EUR][1000 genomes]
rs12492904	0.96[CEU][hapmap]
rs13075955	0.84[EUR][1000 genomes]
rs13094293	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs1349262	0.96[CEU][hapmap];0.80[CHB][hapmap];0.80[EUR][1000 genomes]
rs13715	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs1449868	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap]
rs1449869	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs1530753	0.96[CEU][hapmap];0.80[CHB][hapmap];0.80[EUR][1000 genomes]
rs1532588	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs1814565	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs1827159	0.96[CEU][hapmap];0.80[CHB][hapmap];0.80[EUR][1000 genomes]
rs1839406	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs1868569	0.81[EUR][1000 genomes]
rs1868570	0.81[EUR][1000 genomes]
rs1965343	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs2045306	0.80[EUR][1000 genomes]
rs2124541	0.96[CEU][hapmap];0.80[CHB][hapmap];0.89[GIH][hapmap];0.80[TSI][hapmap]
rs2124543	0.96[CEU][hapmap]
rs2137586	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2175739	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2290549	0.85[CEU][hapmap];0.80[CHB][hapmap]
rs2353408	0.81[EUR][1000 genomes]
rs2353409	0.80[EUR][1000 genomes]
rs2353411	0.96[CEU][hapmap];0.80[CHB][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs3821645	0.96[CEU][hapmap];0.80[CHB][hapmap];0.80[EUR][1000 genomes]
rs3856697	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs3902877	0.96[CEU][hapmap]
rs4030582	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs4683721	0.81[EUR][1000 genomes]
rs4683722	0.96[CEU][hapmap]
rs4683723	0.82[EUR][1000 genomes]
rs4683724	0.80[EUR][1000 genomes]
rs6440129	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs6440134	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs6781887	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs6784200	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6805417	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap]
rs6808406	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6808689	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs7611721	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap]
rs7623532	0.81[EUR][1000 genomes]
rs7648143	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7652745	0.85[CEU][hapmap];0.80[CHB][hapmap]
rs766360	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs936194	0.80[EUR][1000 genomes]
rs936197	0.84[EUR][1000 genomes]
rs937498	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs9814656	0.92[CEU][hapmap];0.80[CHB][hapmap];0.81[EUR][1000 genomes]
rs9816317	0.80[EUR][1000 genomes]
rs9820175	0.94[EUR][1000 genomes]
rs9831162	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9835348	0.96[CEU][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap]
rs9847059	0.82[EUR][1000 genomes]
rs9851353	0.81[EUR][1000 genomes]
rs9862433	0.80[EUR][1000 genomes]
rs9875210	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11709036	CHST2	cis	parietal	SCAN
rs11709036	SLC9A9	cis	parietal	SCAN
rs11709036	SR140	Cis_1M	lymphoblastoid	RTeQTL
rs11709036	U2SURP	cis	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142804400-142809400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:142807800-142811000	Weak transcription	K562	blood
3	chr3:142809000-142810200	Enhancers	Fetal Brain Male	brain
4	chr3:142809200-142809600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:142809200-142809800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:142809200-142809800	Enhancers	HSMM	muscle
7	chr3:142809200-142809800	Enhancers	HSMMtube	muscle
8	chr3:142809200-142810200	Enhancers	Cortex derived primary cultured neurospheres	brain

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