Variant report

Variant	rs12431625
Chromosome Location	chr14:104360609-104360610
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:104354468..104357405-chr14:104359410..104362163,3	MCF-7	breast:
2	chr14:104311422..104315545-chr14:104356597..104360992,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TDRD9-3	chr14:104358583-104361100	l_1075_NR_024396

Variant related genes	Relation type
ENSG00000088808	Chromatin interaction
ENSG00000258735	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10140292	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10140390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10145882	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12437404	0.88[AMR][1000 genomes]
rs17101922	0.84[AMR][1000 genomes]
rs2003053	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28493894	0.84[AMR][1000 genomes]
rs28720127	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28736513	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34606901	0.84[AMR][1000 genomes]
rs4906381	0.82[AMR][1000 genomes]
rs4906384	0.84[AMR][1000 genomes]
rs4906386	0.82[AMR][1000 genomes]
rs55920546	0.88[AMR][1000 genomes]
rs56817754	0.82[AMR][1000 genomes]
rs58701300	0.82[AMR][1000 genomes]
rs58887008	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs60242182	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7149148	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73350570	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8009847	0.84[AMR][1000 genomes]
rs8022769	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	esv2758368	chr14:104147525-104412813	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2760013	chr14:104147525-104412813	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv902313	chr14:104162263-104378087	Bivalent Enhancer Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv902318	chr14:104255083-104464809	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv902319	chr14:104255083-104620077	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
8	nsv902321	chr14:104283104-104378087	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1053305	chr14:104326137-104372608	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv542205	chr14:104326137-104372608	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv542206	chr14:104326137-104377507	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1042792	chr14:104326137-104384260	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv542207	chr14:104326137-104384260	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv9174	chr14:104352172-104362943	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	esv3328741	chr14:104359249-104362147	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104347000-104362800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr14:104347200-104362800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:104353600-104362800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr14:104355800-104362200	Enhancers	Liver	Liver
5	chr14:104356000-104362400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:104356400-104362800	Weak transcription	NHEK	skin
7	chr14:104356800-104364000	Weak transcription	HMEC	breast
8	chr14:104357600-104362800	Weak transcription	Small Intestine	intestine
9	chr14:104357800-104363000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr14:104357800-104363400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr14:104358000-104360800	Weak transcription	Right Ventricle	heart
12	chr14:104358400-104360800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr14:104360000-104362000	Enhancers	Pancreas	Pancrea
14	chr14:104360000-104363000	Enhancers	Duodenum Mucosa	Duodenum
15	chr14:104360000-104363000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr14:104360000-104363000	Enhancers	HepG2	liver
17	chr14:104360200-104361000	Enhancers	Colonic Mucosa	Colon
18	chr14:104360200-104361200	Enhancers	Placenta	Placenta
19	chr14:104360200-104361400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr14:104360200-104361400	Enhancers	Hela-S3	cervix
21	chr14:104360200-104361600	Enhancers	Spleen	Spleen
22	chr14:104360200-104362000	Enhancers	Esophagus	oesophagus
23	chr14:104360200-104362000	Enhancers	Gastric	stomach
24	chr14:104360200-104362200	Enhancers	Fetal Intestine Large	intestine
25	chr14:104360200-104362200	Enhancers	Fetal Intestine Small	intestine
26	chr14:104360200-104362800	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr14:104360200-104362800	Enhancers	Stomach Mucosa	stomach
28	chr14:104360400-104363400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr14:104360600-104360800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr14:104360600-104361000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr14:104360600-104361200	Enhancers	Left Ventricle	heart
32	chr14:104360600-104361400	Enhancers	Lung	lung

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