Variant report

Variant	rs11678684
Chromosome Location	chr2:233742837-233742838
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:233741247..233743514-chr2:233891035..233893052,2	MCF-7	breast:
2	chr2:233739591..233745527-chr2:233747956..233752237,8	MCF-7	breast:
3	chr2:233741423..233744026-chr2:234158649..234161710,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066248	Chromatin interaction
ENSG00000085978	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10933410	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11683827	0.86[CEU][hapmap]
rs12463466	0.85[CEU][hapmap]
rs12477794	0.85[CEU][hapmap]
rs1554218	1.00[CEU][hapmap];0.81[AMR][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	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	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv984452	chr2:233725452-233762965	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv999116	chr2:233733352-233759864	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1007029	chr2:233733352-233760519	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv536179	chr2:233735380-233757170	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11678684	DEGS1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233726800-233755600	Weak transcription	HSMMtube	muscle
2	chr2:233741200-233743000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:233741600-233745000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:233741600-233747000	Weak transcription	Gastric	stomach
5	chr2:233741600-233747600	Weak transcription	NHLF	lung
6	chr2:233741600-233749600	Weak transcription	Pancreas	Pancrea
7	chr2:233741800-233743000	Enhancers	Brain Substantia Nigra	brain
8	chr2:233741800-233743000	Weak transcription	Esophagus	oesophagus
9	chr2:233741800-233750000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:233742000-233749000	Weak transcription	Small Intestine	intestine
11	chr2:233742200-233743200	Transcr. at gene 5' and 3'	HepG2	liver
12	chr2:233742200-233745200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:233742200-233747400	Weak transcription	Fetal Brain Female	brain
14	chr2:233742200-233749800	Weak transcription	Brain Germinal Matrix	brain
15	chr2:233742200-233750000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:233742200-233750800	Weak transcription	Fetal Brain Male	brain
17	chr2:233742400-233743600	Enhancers	Liver	Liver
18	chr2:233742400-233743800	Enhancers	Brain Angular Gyrus	brain
19	chr2:233742400-233745200	Enhancers	Brain Cingulate Gyrus	brain
20	chr2:233742400-233752400	Weak transcription	Colonic Mucosa	Colon
21	chr2:233742400-233754200	Strong transcription	Fetal Intestine Small	intestine
22	chr2:233742400-233755600	Weak transcription	Fetal Intestine Large	intestine
23	chr2:233742600-233743200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:233742600-233744400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:233742600-233745800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:233742600-233753400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr2:233742800-233743000	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr2:233742800-233743000	Enhancers	Brain Hippocampus Middle	brain
29	chr2:233742800-233743000	Flanking Active TSS	A549	lung
30	chr2:233742800-233743200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:233742800-233744600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:233742800-233746000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:233742800-233755600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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