Variant report

Variant	rs12744338
Chromosome Location	chr1:246734487-246734488
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	SPI1	chr1:246734473-246735121	GM12878	blood:	n/a	chr1:246734846-246734859 chr1:246734847-246734856

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246728909..246731573-chr1:246733348..246738076,5	MCF-7	breast:
2	chr1:246727699..246730587-chr1:246733873..246736383,3	MCF-7	breast:

Variant related genes	Relation type
TFB2M	TF binding region
ENSG00000162851	Chromatin interaction
ENSG00000162852	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12742513	0.84[ASN][1000 genomes]
rs12742618	0.83[ASN][1000 genomes]
rs12746341	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12748061	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12750641	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3795474	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7536768	0.85[ASN][1000 genomes]
rs7547043	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1000654	chr1:245966390-246778182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv535392	chr1:245966390-246778182	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv948348	chr1:246090818-246853200	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv430402	chr1:246124959-246787448	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv497890	chr1:246143172-246778453	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1005573	chr1:246378676-246740427	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv535405	chr1:246378676-246740427	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2757779	chr1:246407146-246740944	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
13	esv2759012	chr1:246407146-246740944	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv428346	chr1:246407146-246740944	Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv1013800	chr1:246472691-246840960	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
16	nsv535409	chr1:246472691-246840960	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
17	esv2762191	chr1:246546436-246815064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
19	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
20	nsv1010453	chr1:246645797-246815052	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	nsv998579	chr1:246666041-246817877	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	nsv1010316	chr1:246686301-246840960	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
23	nsv535414	chr1:246686301-246840960	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
24	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
25	nsv522963	chr1:246696596-246747586	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
26	nsv527464	chr1:246698653-246742157	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
27	nsv873420	chr1:246706139-246755124	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
28	nsv528615	chr1:246708467-246843315	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
29	nsv1014280	chr1:246709243-246823255	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
30	nsv1013264	chr1:246723012-246807400	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
31	nsv535415	chr1:246723012-246807400	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
32	nsv1005214	chr1:246730885-246841107	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246730600-246735000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:246730600-246737600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:246730800-246744000	Weak transcription	Ovary	ovary
4	chr1:246731000-246737600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:246731000-246742000	Weak transcription	Fetal Stomach	stomach
6	chr1:246731000-246747000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:246731200-246734600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr1:246731400-246734800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:246731400-246740600	Weak transcription	HSMMtube	muscle
10	chr1:246731400-246742000	Weak transcription	NH-A	brain
11	chr1:246731400-246746000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:246731400-246746200	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:246731400-246747200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:246731400-246753400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:246731600-246741600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:246731600-246747000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:246732000-246746400	Weak transcription	Hela-S3	cervix
18	chr1:246732000-246747600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:246732600-246734600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:246732600-246735000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:246732600-246735200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr1:246732600-246735400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr1:246732600-246735400	Enhancers	Colon Smooth Muscle	Colon
24	chr1:246732600-246735800	Enhancers	NHDF-Ad	bronchial
25	chr1:246733000-246736800	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr1:246733200-246734600	Weak transcription	Fetal Thymus	thymus
27	chr1:246733200-246735000	Weak transcription	Right Atrium	heart
28	chr1:246733200-246735200	Transcr. at gene 5' and 3'	K562	blood
29	chr1:246733200-246735600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr1:246733200-246740600	Weak transcription	Liver	Liver
31	chr1:246733200-246740800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:246733200-246741000	Weak transcription	NHLF	lung
33	chr1:246733200-246741400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:246733200-246745600	Weak transcription	Pancreas	Pancrea
35	chr1:246733200-246746000	Weak transcription	Lung	lung
36	chr1:246733200-246747000	Weak transcription	NHEK	skin
37	chr1:246733400-246736200	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr1:246733400-246738000	Enhancers	Primary B cells from peripheral blood	blood
39	chr1:246733400-246741000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:246733400-246746800	Weak transcription	Brain Angular Gyrus	brain
41	chr1:246733600-246734800	Enhancers	HUVEC	blood vessel
42	chr1:246733600-246735000	Weak transcription	Adipose Nuclei	Adipose
43	chr1:246733600-246735000	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:246733600-246735000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:246733600-246735000	Weak transcription	Spleen	Spleen
46	chr1:246733600-246736400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:246733600-246737800	Weak transcription	Osteobl	bone
48	chr1:246733600-246740000	Weak transcription	Right Ventricle	heart
49	chr1:246733600-246740600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:246733600-246742000	Weak transcription	Fetal Intestine Small	intestine

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