Variant report

Variant	rs12404571
Chromosome Location	chr1:245848323-245848324
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:245842274..245845085-chr1:245848041..245849884,2	MCF-7	breast:
2	chr1:245848290..245848810-chr6:160211092..160212029,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000112110	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12403283	0.95[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3806273	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3820246	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58427858	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007728	chr1:245235174-246156455	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1014558	chr1:245316147-245862041	Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1002499	chr1:245365351-245929051	Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv497871	chr1:245706209-246655353	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv534412	chr1:245747724-246655416	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv3403138	chr1:245793113-245892931	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1003594	chr1:245801793-246649329	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv521141	chr1:245822899-245863222	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2752867	chr1:245829959-245932959	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1004412	chr1:245830921-246169054	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv535385	chr1:245830921-246169054	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv517510	chr1:245847034-245863222	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv827698	chr1:245847754-245853707	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:245815200-245848400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:245835600-245848400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:245836000-245848400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:245839800-245849600	Weak transcription	Gastric	stomach
5	chr1:245841400-245856200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:245843200-245851200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:245844200-245851000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:245844200-245870400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:245846000-245848400	Enhancers	Fetal Lung	lung
10	chr1:245846200-245848400	Enhancers	Fetal Muscle Leg	muscle
11	chr1:245846200-245848600	Enhancers	Fetal Brain Male	brain
12	chr1:245846400-245848400	Enhancers	Fetal Muscle Trunk	muscle
13	chr1:245846400-245848800	Enhancers	Right Ventricle	heart
14	chr1:245846600-245854200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:245847000-245849800	Weak transcription	Right Atrium	heart
16	chr1:245847000-245851000	Weak transcription	NHLF	lung
17	chr1:245847200-245848400	Weak transcription	Fetal Intestine Large	intestine
18	chr1:245847200-245848600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:245847200-245848600	Enhancers	Fetal Heart	heart
20	chr1:245847200-245848600	Weak transcription	Fetal Intestine Small	intestine
21	chr1:245847400-245848600	Weak transcription	Fetal Brain Female	brain
22	chr1:245847400-245852400	Weak transcription	Lung	lung
23	chr1:245847400-245855200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:245847600-245853800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:245847800-245850400	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr1:245847800-245852600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:245847800-245853600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:245848000-245848400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:245848000-245848400	Weak transcription	Spleen	Spleen
30	chr1:245848000-245848800	Weak transcription	Brain Germinal Matrix	brain
31	chr1:245848000-245851400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:245848200-245850000	Weak transcription	Brain Substantia Nigra	brain
33	chr1:245848200-245850000	Strong transcription	Placenta	Placenta
34	chr1:245848200-245850000	Strong transcription	Fetal Stomach	stomach
35	chr1:245848200-245850200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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