Variant report

Variant	rs4614979
Chromosome Location	chr2:98856008-98856009
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98849964..98853776-chr2:98854233..98857105,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168658	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11124119	0.83[ASN][1000 genomes]
rs11889349	0.80[ASN][1000 genomes]
rs11891512	0.80[ASN][1000 genomes]
rs12478763	0.80[ASN][1000 genomes]
rs12478769	0.80[ASN][1000 genomes]
rs12993718	0.80[ASN][1000 genomes]
rs13013876	0.80[ASN][1000 genomes]
rs13033263	0.80[ASN][1000 genomes]
rs17029642	1.00[AFR][1000 genomes]
rs4374424	0.80[ASN][1000 genomes]
rs4477970	0.80[ASN][1000 genomes]
rs4479470	0.80[ASN][1000 genomes]
rs4494805	0.80[ASN][1000 genomes]
rs4632400	0.80[ASN][1000 genomes]
rs4851952	0.80[ASN][1000 genomes]
rs4851953	0.83[ASN][1000 genomes]
rs4851958	1.00[AFR][1000 genomes]
rs6543419	0.80[ASN][1000 genomes]
rs6747410	0.83[ASN][1000 genomes]
rs72950941	0.90[ASN][1000 genomes]
rs7574218	0.80[ASN][1000 genomes]
rs7578802	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv582513	chr2:98829237-98869914	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv582514	chr2:98835962-98869914	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1014147	chr2:98855007-98878044	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv818075	chr2:98855497-98872039	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv582515	chr2:98855497-98885925	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv517669	chr2:98855497-98889961	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv437289	chr2:98855497-98891519	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4614979	TRBC1///TRBV19///TRBV3-1///TRBV5-4///TRBV7	trans	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98851000-98857600	Weak transcription	Brain Substantia Nigra	brain
2	chr2:98851400-98856800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:98851600-98856800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:98854200-98857400	Weak transcription	Placenta	Placenta
5	chr2:98854400-98857400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:98855600-98857800	Weak transcription	Fetal Brain Male	brain

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