Variant report

Variant	rs404751
Chromosome Location	chr12:50473660-50473661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr12:50473624-50473925	Hela-S3	cervix:	n/a	chr12:50473629-50473637
2	REST	chr12:50473640-50473845	HepG2	liver:	n/a	n/a
3	REST	chr12:50473554-50473899	PANC-1	pancreas:	n/a	chr12:50473629-50473637
4	REST	chr12:50473567-50473983	MCF-7	breast:	n/a	chr12:50473629-50473637
5	RCOR1	chr12:50473650-50473663	HepG2	liver:	n/a	n/a
6	REST	chr12:50473549-50473946	U87	brain:	n/a	chr12:50473629-50473637
7	REST	chr12:50473535-50473934	PFSK-1	brain:	n/a	chr12:50473629-50473637
8	REST	chr12:50473459-50473999	A549	lung:	n/a	chr12:50473629-50473637
9	REST	chr12:50473609-50473890	HepG2	liver:	n/a	chr12:50473629-50473637
10	REST	chr12:50473539-50473985	K562	blood:	n/a	chr12:50473629-50473637
11	REST	chr12:50473522-50473914	H1-hESC	embryonic stem cell:	n/a	chr12:50473629-50473637
12	REST	chr12:50473529-50474012	PANC-1	pancreas:	n/a	chr12:50473629-50473637
13	REST	chr12:50473569-50473924	A549	lung:	n/a	chr12:50473629-50473637
14	REST	chr12:50473522-50473989	PFSK-1	brain:	n/a	chr12:50473629-50473637
15	REST	chr12:50473540-50473930	SK-N-SH	brain:	n/a	chr12:50473629-50473637
16	REST	chr12:50473496-50474034	HL-60	blood:	n/a	chr12:50473629-50473637
17	REST	chr12:50473616-50473888	SK-N-SH	brain:	n/a	chr12:50473629-50473637
18	REST	chr12:50473519-50473982	PANC-1	pancreas:	n/a	chr12:50473629-50473637
19	REST	chr12:50473351-50474121	ECC-1	luminal epithelium:	n/a	chr12:50473629-50473637
20	TEAD4	chr12:50473507-50473987	A549	lung:	n/a	n/a
21	REST	chr12:50473532-50473990	HL-60	blood:	n/a	chr12:50473629-50473637
22	REST	chr12:50473579-50473874	U87	brain:	n/a	chr12:50473629-50473637
23	REST	chr12:50473598-50473877	GM12878	blood:	n/a	chr12:50473629-50473637
24	REST	chr12:50473489-50473967	MCF-7	breast:	n/a	chr12:50473629-50473637
25	REST	chr12:50473627-50473837	U87	brain:	n/a	chr12:50473629-50473637
26	REST	chr12:50473649-50473872	K562	blood:	n/a	n/a
27	REST	chr12:50473561-50473933	H1-hESC	embryonic stem cell:	n/a	chr12:50473629-50473637
28	REST	chr12:50473602-50473900	Hela-S3	cervix:	n/a	chr12:50473629-50473637
29	REST	chr12:50473488-50473961	HepG2	liver:	n/a	chr12:50473629-50473637
30	REST	chr12:50473648-50473801	PFSK-1	brain:	n/a	n/a
31	REST	chr12:50473339-50474125	ECC-1	luminal epithelium:	n/a	chr12:50473629-50473637
32	REST	chr12:50473612-50473849	HepG2	liver:	n/a	chr12:50473629-50473637
33	REST	chr12:50473569-50473888	PANC-1	pancreas:	n/a	chr12:50473629-50473637

No.	Distal block	Cell Line	Cell type
1	chr12:50450867..50453197-chr12:50472058..50474772,2	MCF-7	breast:
2	chr12:50466696..50474949-chr12:50474970..50481457,17	MCF-7	breast:
3	chr12:50472028..50474859-chr12:50477717..50480636,3	MCF-7	breast:
4	chr12:50471491..50474468-chr12:50505629..50507284,2	K562	blood:
5	chr12:50465539..50467962-chr12:50472151..50474107,2	K562	blood:
6	chr12:50471856..50474200-chr12:50488886..50490561,2	K562	blood:

Variant related genes	Relation type
ASIC1	TF binding region
ENSG00000066117	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs17124514	1.00[CEU][hapmap]
rs376184	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs386469	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs393848	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs439171	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs450423	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs484951	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4898546	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs590460	0.89[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs613066	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs627869	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs627887	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs653576	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs685012	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs706789	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs706794	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs835591	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs835593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835594	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836178	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs836184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs836185	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs836186	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs844359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs860699	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS 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 miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50458200-50478200	Weak transcription	Thymus	Thymus
2	chr12:50464400-50478200	Weak transcription	Fetal Heart	heart
3	chr12:50464400-50478200	Weak transcription	Right Atrium	heart
4	chr12:50464800-50474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:50464800-50478200	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:50464800-50478200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:50464800-50478200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:50464800-50478400	Weak transcription	Primary T cells from cord blood	blood
9	chr12:50466800-50474800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:50469400-50474400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:50469400-50474800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:50469400-50474800	Weak transcription	Right Ventricle	heart
13	chr12:50469400-50478200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:50469400-50478200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:50469400-50478200	Weak transcription	Fetal Brain Male	brain
16	chr12:50469600-50474400	Weak transcription	K562	blood
17	chr12:50469600-50474600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:50469600-50474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:50469600-50477000	Strong transcription	Fetal Brain Female	brain
20	chr12:50469600-50477600	Weak transcription	HMEC	breast
21	chr12:50469600-50478200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:50469600-50478200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:50469600-50478200	Weak transcription	Brain Angular Gyrus	brain
24	chr12:50469600-50478200	Weak transcription	Brain Anterior Caudate	brain
25	chr12:50469600-50478200	Weak transcription	Fetal Lung	lung
26	chr12:50469600-50478200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:50469800-50476000	Weak transcription	Colonic Mucosa	Colon
28	chr12:50469800-50478200	Weak transcription	Gastric	stomach
29	chr12:50470000-50478200	Weak transcription	Liver	Liver
30	chr12:50470600-50474600	Strong transcription	Fetal Stomach	stomach
31	chr12:50471200-50474000	Strong transcription	Brain Hippocampus Middle	brain
32	chr12:50471200-50476200	Strong transcription	Brain Germinal Matrix	brain
33	chr12:50471400-50477600	Weak transcription	GM12878-XiMat	blood
34	chr12:50471600-50474800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:50471800-50474800	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr12:50472200-50475600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:50472600-50478000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:50472600-50478200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:50473400-50475800	Enhancers	HepG2	liver
40	chr12:50473400-50478200	Enhancers	Fetal Intestine Large	intestine
41	chr12:50473600-50473800	Enhancers	Lung	lung
42	chr12:50473600-50474800	Weak transcription	Fetal Muscle Leg	muscle
43	chr12:50473600-50475800	Enhancers	Fetal Intestine Small	intestine

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