Variant report

Variant	rs13410790
Chromosome Location	chr2:97557872-97557873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97556750..97558871-chr2:97588696..97591655,2	MCF-7	breast:
2	chr2:97556985..97558977-chr2:97588786..97591585,2	K562	blood:
3	chr2:97497342..97499040-chr2:97557166..97559196,2	MCF-7	breast:
4	chr2:97490386..97492773-chr2:97557628..97559451,2	MCF-7	breast:
5	chr2:97557540..97561219-chr2:97615825..97618671,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168754	Chromatin interaction
ENSG00000168763	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10169387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182668	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs10182965	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11677797	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11694296	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12613171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13421275	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13423092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13425281	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2314650	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs28687044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4907203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4907204	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907205	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4907206	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4907256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907258	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907259	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4907260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61382911	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
8	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
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97552600-97560800	Weak transcription	Hela-S3	cervix
2	chr2:97554200-97560800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:97554400-97561000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:97554400-97563400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:97554600-97563400	Weak transcription	Fetal Heart	heart
6	chr2:97554800-97559200	Weak transcription	NHEK	skin
7	chr2:97554800-97561200	Weak transcription	Fetal Brain Female	brain
8	chr2:97555000-97560800	Weak transcription	Fetal Brain Male	brain
9	chr2:97555000-97561200	Weak transcription	Pancreas	Pancrea
10	chr2:97555600-97559800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:97555800-97558400	Enhancers	Ovary	ovary
12	chr2:97555800-97559800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:97556000-97558000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:97556000-97558000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:97556000-97558200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr2:97556000-97558800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:97556000-97559000	Enhancers	Colon Smooth Muscle	Colon
18	chr2:97556000-97559400	Enhancers	Lung	lung
19	chr2:97556000-97560000	Transcr. at gene 5' and 3'	K562	blood
20	chr2:97556000-97560200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:97556000-97560200	Enhancers	Brain Hippocampus Middle	brain
22	chr2:97556000-97562200	Enhancers	Brain Anterior Caudate	brain
23	chr2:97556200-97558000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:97556200-97558000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:97556200-97558000	Enhancers	Left Ventricle	heart
26	chr2:97556200-97558000	Enhancers	HSMMtube	muscle
27	chr2:97556200-97558200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:97556200-97558200	Enhancers	HSMM	muscle
29	chr2:97556200-97558400	Enhancers	Stomach Smooth Muscle	stomach
30	chr2:97556200-97558600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr2:97556200-97558600	Enhancers	Fetal Lung	lung
32	chr2:97556200-97558600	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr2:97556200-97558800	Enhancers	Fetal Stomach	stomach
34	chr2:97556200-97559200	Enhancers	Adipose Nuclei	Adipose
35	chr2:97556200-97559600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr2:97556200-97559800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr2:97556200-97560000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr2:97556200-97560000	Enhancers	Psoas Muscle	Psoas
39	chr2:97556200-97560200	Enhancers	Primary T cells from cord blood	blood
40	chr2:97556200-97560200	Enhancers	Brain Angular Gyrus	brain
41	chr2:97556200-97560200	Enhancers	Brain Substantia Nigra	brain
42	chr2:97556200-97562200	Enhancers	Brain Cingulate Gyrus	brain
43	chr2:97556200-97562400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr2:97556400-97558000	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr2:97556400-97558000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr2:97556400-97558000	Enhancers	Esophagus	oesophagus
47	chr2:97556400-97558200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr2:97556400-97558400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:97556400-97558400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:97556400-97558400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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