Variant report

Variant	rs4742406
Chromosome Location	chr9:7756067-7756068
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12344462	0.82[EUR][1000 genomes]
rs12552665	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13298310	0.83[EUR][1000 genomes]
rs1332899	0.85[EUR][1000 genomes]
rs17546550	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2151230	0.94[EUR][1000 genomes]
rs7466661	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34566	chr9:7291742-7781370	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv818681	chr9:7292836-7781365	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1033077	chr9:7358832-7990735	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv539977	chr9:7358832-7990735	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1029032	chr9:7431547-7764888	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv613266	chr9:7588854-7901308	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv995116	chr9:7682729-8065192	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1015192	chr9:7730407-7772496	Weak transcription Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1017021	chr9:7731398-7764735	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1016692	chr9:7731398-7772496	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1034997	chr9:7731398-7773114	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1035009	chr9:7732196-7770825	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv519687	chr9:7734250-7770942	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv466120	chr9:7734250-7770942	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv613268	chr9:7734250-7770942	Weak transcription Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv429989	chr9:7735280-7774180	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv429990	chr9:7735283-7770233	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv1025200	chr9:7735283-7772912	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv1022474	chr9:7735724-7770825	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv613269	chr9:7742476-7759331	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
21	nsv892212	chr9:7742476-7787532	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4742406	RCL1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7755000-7756400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:7755400-7756400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr9:7755600-7756600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:7755600-7756800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr9:7755800-7757200	Enhancers	GM12878-XiMat	blood
6	chr9:7756000-7756600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:7756000-7756800	Enhancers	Primary T helper cells PMA-I stimulated	--

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