Variant report

Variant	rs56361249
Chromosome Location	chr2:97380229-97380230
allele	G/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	SIN3AK20	chr2:97380010-97380764	MCF-7	breast:	n/a	n/a
2	GATA3	chr2:97380110-97380694	MCF-7	breast:	n/a	n/a
3	SIN3AK20	chr2:97380149-97380809	MCF-7	breast:	n/a	n/a
4	ZNF217	chr2:97380192-97380582	MCF-7	breast:	n/a	n/a
5	GATA3	chr2:97379989-97380687	MCF-7	breast:	n/a	n/a
6	GATA3	chr2:97380030-97380681	MCF-7	breast:	n/a	n/a
7	HDAC2	chr2:97380217-97380758	MCF-7	breast:	n/a	n/a
8	GATA3	chr2:97380222-97380662	T-47D	breast:	n/a	n/a
9	POLR2A	chr2:97379989-97380288	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:97368361..97369984-chr2:97379987..97381793,2	K562	blood:
2	chr2:97380151..97383918-chr2:97384122..97387613,5	K562	blood:
3	chr2:97360914..97363341-chr2:97377649..97380525,2	MCF-7	breast:

Variant related genes	Relation type
LMAN2L	TF binding region
ENSG00000249715	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2271893	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2314398	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4619651	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56351161	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58361269	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6746896	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67570263	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72809820	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72809827	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72809838	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription 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	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv469775	chr2:97240926-97412491	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv482586	chr2:97240926-97412491	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv834306	chr2:97241115-97412938	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
14	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
15	nsv834307	chr2:97321447-97479266	Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97360800-97381200	Strong transcription	Fetal Stomach	stomach
2	chr2:97365000-97389400	Strong transcription	Fetal Muscle Trunk	muscle
3	chr2:97365200-97387000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:97365400-97382400	Strong transcription	Primary T cells from cord blood	blood
5	chr2:97365600-97380400	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:97367400-97382600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:97367600-97381000	Strong transcription	HepG2	liver
8	chr2:97367800-97382800	Strong transcription	Brain Anterior Caudate	brain
9	chr2:97368200-97382600	Strong transcription	Fetal Thymus	thymus
10	chr2:97368400-97405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:97368600-97383200	Strong transcription	Brain Cingulate Gyrus	brain
12	chr2:97370200-97382400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:97370400-97380400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:97370600-97380600	Strong transcription	Adipose Nuclei	Adipose
15	chr2:97370600-97398800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:97370800-97381600	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:97372400-97400000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:97373200-97399000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:97373400-97395000	Weak transcription	Small Intestine	intestine
20	chr2:97375200-97380800	Strong transcription	Brain Angular Gyrus	brain
21	chr2:97375600-97380400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:97375600-97383200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:97375600-97383400	Strong transcription	Fetal Lung	lung
24	chr2:97375600-97398600	Weak transcription	Psoas Muscle	Psoas
25	chr2:97376000-97380600	Strong transcription	Fetal Brain Female	brain
26	chr2:97376000-97382600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:97376000-97383000	Strong transcription	Primary B cells from cord blood	blood
28	chr2:97376000-97385000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:97376000-97404000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:97376200-97393400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:97377000-97393200	Weak transcription	HUVEC	blood vessel
32	chr2:97377000-97393200	Weak transcription	NH-A	brain
33	chr2:97377200-97393000	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:97377200-97393000	Weak transcription	HSMMtube	muscle
35	chr2:97377200-97393200	Weak transcription	HMEC	breast
36	chr2:97377200-97393400	Weak transcription	Hela-S3	cervix
37	chr2:97377400-97393200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:97377400-97393200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:97377400-97393400	Weak transcription	HSMM	muscle
40	chr2:97377600-97393200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:97377600-97393200	Weak transcription	NHDF-Ad	bronchial
42	chr2:97377600-97396200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:97377600-97398000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:97377600-97398800	Weak transcription	K562	blood
45	chr2:97377600-97399600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:97377800-97381400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:97377800-97382000	Weak transcription	Fetal Kidney	kidney
48	chr2:97377800-97387000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:97377800-97388200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:97377800-97389000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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