Variant report

Variant	rs778354
Chromosome Location	chr2:233785015-233785016
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	chr2:233784593..233788335-chr2:233796578..233799321,3	K562	blood:
2	chr2:233777266..233779765-chr2:233782803..233785720,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1878288	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2344912	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778356	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778360	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3377192	chr2:233758324-233835472	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1014548	chr2:233777859-233816018	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs778354	SH3BP4	cis	cerebellum	SCAN
rs778354	TRPM8	cis	cerebellum	SCAN
rs778354	NGEF	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233767000-233789000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:233767200-233790400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:233777000-233787200	Weak transcription	Brain Angular Gyrus	brain
4	chr2:233777400-233789800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:233780000-233789400	Weak transcription	HSMMtube	muscle
6	chr2:233781800-233789800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:233781800-233791800	Weak transcription	Pancreas	Pancrea
8	chr2:233783800-233785600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:233783800-233786800	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr2:233784000-233785600	Strong transcription	Duodenum Mucosa	Duodenum
11	chr2:233784000-233791400	Strong transcription	Liver	Liver
12	chr2:233784200-233789200	Weak transcription	Colonic Mucosa	Colon
13	chr2:233784400-233785200	Active TSS	Brain Anterior Caudate	brain
14	chr2:233784400-233785200	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:233784400-233785600	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr2:233784400-233787000	Strong transcription	Fetal Intestine Small	intestine
17	chr2:233784600-233785200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:233784800-233786400	Weak transcription	HepG2	liver
19	chr2:233785000-233789200	Weak transcription	Esophagus	oesophagus
20	chr2:233785000-233792000	Weak transcription	Gastric	stomach

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