Variant report

Variant	rs4676684
Chromosome Location	chr3:121340536-121340537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121339257..121341104-chr3:121379300..121381638,2	K562	blood:

Variant related genes	Relation type
ENSG00000180353	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12631824	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13067629	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1492177	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1574655	0.88[EUR][1000 genomes]
rs1574735	0.88[EUR][1000 genomes]
rs1873645	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1919552	0.87[EUR][1000 genomes]
rs1919557	0.89[EUR][1000 genomes]
rs1986874	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2001390	0.88[EUR][1000 genomes]
rs2001391	0.88[EUR][1000 genomes]
rs2070179	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2840143	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35295338	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3772127	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4478028	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4676685	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4676686	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6438645	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6791896	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6792659	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6794341	0.88[EUR][1000 genomes]
rs6794677	0.86[EUR][1000 genomes]
rs6802033	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6803839	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6807711	0.91[EUR][1000 genomes]
rs7375038	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7429247	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7430165	0.92[EUR][1000 genomes]
rs7611913	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7620842	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7646585	0.91[EUR][1000 genomes]
rs9289172	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9289173	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9809114	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9812411	0.91[EUR][1000 genomes]
rs9829053	0.86[EUR][1000 genomes]
rs9832267	0.91[EUR][1000 genomes]
rs9835182	0.88[EUR][1000 genomes]
rs9854052	0.91[EUR][1000 genomes]
rs9861992	0.90[EUR][1000 genomes]
rs9864907	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9876021	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998555	chr3:120700604-121348015	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv877381	chr3:121192350-121343500	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1007522	chr3:121200563-121374051	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv999349	chr3:121253990-121360206	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4676684	HCLS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121327200-121343200	Weak transcription	Psoas Muscle	Psoas
2	chr3:121329200-121341200	Weak transcription	Right Atrium	heart
3	chr3:121336400-121342000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:121338000-121341200	Strong transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:121338000-121341600	Strong transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:121338800-121342000	Strong transcription	Fetal Heart	heart
7	chr3:121340200-121340600	Strong transcription	Left Ventricle	heart
8	chr3:121340400-121340800	Enhancers	Spleen	Spleen
9	chr3:121340400-121341800	Genic enhancers	Right Ventricle	heart

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