Variant report

Variant	rs2254675
Chromosome Location	chr12:121408234-121408235
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	chr12:121401463..121403474-chr12:121406949..121408762,2	K562	blood:
2	chr12:121403725..121406245-chr12:121406756..121408586,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf43-1	chr12:121407641-121410095	ENSG00000241388.2
2	lnc-C12orf43-1	chr12:121408046-121410443	NONHSAT031257

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1169285	0.95[YRI][hapmap]
rs1169287	0.95[YRI][hapmap]
rs1169293	0.95[YRI][hapmap]
rs2245407	0.95[YRI][hapmap]
rs2251573	0.94[AFR][1000 genomes]
rs2255041	0.97[AFR][1000 genomes]
rs672632	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	esv3357747	chr12:121405281-121427388	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121400600-121416000	Weak transcription	Small Intestine	intestine
2	chr12:121403200-121409400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:121403800-121411000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:121404800-121409000	Strong transcription	Fetal Intestine Large	intestine
5	chr12:121404800-121409800	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr12:121405200-121415400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:121405400-121409000	Strong transcription	Pancreas	Pancrea
8	chr12:121405400-121409200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr12:121406600-121408400	Strong transcription	Colonic Mucosa	Colon
10	chr12:121406600-121409000	Strong transcription	Gastric	stomach
11	chr12:121406600-121410800	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr12:121406600-121412400	Genic enhancers	Liver	Liver
13	chr12:121406800-121408400	Strong transcription	Stomach Mucosa	stomach
14	chr12:121407000-121409400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:121407200-121409400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:121407200-121409800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:121407400-121409400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:121407400-121409400	Weak transcription	A549	lung
19	chr12:121407400-121410800	Weak transcription	Fetal Stomach	stomach
20	chr12:121407800-121409200	Strong transcription	HepG2	liver
21	chr12:121408000-121414200	Genic enhancers	Fetal Intestine Small	intestine
22	chr12:121408200-121408400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:121408200-121408400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:121408200-121408400	Enhancers	Esophagus	oesophagus
25	chr12:121408200-121409200	Genic enhancers	Fetal Kidney	kidney
26	chr12:121408200-121409200	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:121408200-121417800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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