Variant report

Variant	rs13401475
Chromosome Location	chr2:10586438-10586439
allele	A/G
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	CHD1	chr2:10586355-10588647	IMR90	lung:	n/a	n/a
2	POLR2A	chr2:10586243-10587139	Hela-S3	cervix:	n/a	n/a
3	STAT1	chr2:10586402-10587093	Hela-S3	cervix:	n/a	chr2:10586605-10586625 chr2:10586609-10586620 chr2:10586611-10586620 chr2:10586605-10586625 chr2:10586611-10586619 chr2:10586596-10586619 chr2:10586610-10586619 chr2:10587054-10587066 chr2:10586608-10586622
4	POLR2A	chr2:10586318-10590638	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr2:10586304-10587231	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:10259653..10265917-chr2:10585320..10590295,8	MCF-7	breast:
2	chr2:10259839..10264771-chr2:10582056..10590038,19	K562	blood:
3	chr2:10584788..10589777-chr2:10826863..10830293,6	K562	blood:
4	chr2:10583602..10586485-chr2:10613524..10616092,2	K562	blood:
5	chr2:10584220..10586892-chr2:10686951..10688711,2	K562	blood:
6	chr2:10259710..10265084-chr2:10586364..10590442,7	MCF-7	breast:
7	chr2:10359472..10362167-chr2:10583974..10586621,2	K562	blood:
8	chr2:10441275..10444094-chr2:10585125..10586626,2	MCF-7	breast:
9	chr2:10191630..10196148-chr2:10586386..10589794,5	K562	blood:
10	chr2:10257984..10265070-chr2:10582045..10589780,17	K562	blood:

Variant related genes	Relation type
ENSG00000257135	TF binding region
ENSG00000171848	Chromatin interaction
ENSG00000271787	Chromatin interaction
ENSG00000272524	Chromatin interaction
ENSG00000115761	Chromatin interaction
ENSG00000115756	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10170147	1.00[EUR][1000 genomes]
rs10189026	1.00[EUR][1000 genomes]
rs10203520	1.00[EUR][1000 genomes]
rs10203529	1.00[EUR][1000 genomes]
rs10490729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11897672	1.00[EUR][1000 genomes]
rs11903106	1.00[EUR][1000 genomes]
rs11904157	1.00[EUR][1000 genomes]
rs11904263	1.00[EUR][1000 genomes]
rs16856239	1.00[EUR][1000 genomes]
rs16856397	1.00[EUR][1000 genomes]
rs1804032	1.00[ASN][1000 genomes]
rs28362383	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28362406	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362407	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28362418	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55955247	1.00[ASN][1000 genomes]
rs58248202	1.00[EUR][1000 genomes]
rs59876692	1.00[EUR][1000 genomes]
rs61684351	1.00[EUR][1000 genomes]
rs6738288	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73163017	1.00[EUR][1000 genomes]
rs73917006	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873645	chr2:10537347-10612091	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv873646	chr2:10550517-10612091	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	esv1840383	chr2:10569021-10588903	Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv873647	chr2:10576424-10597858	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription 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	45 gene(s)	inside rSNPs	diseases
7	nsv873648	chr2:10584639-10599493	Active TSS Strong transcription Enhancers Flanking Active TSS Weak 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	42 gene(s)	inside rSNPs	diseases
8	esv1819730	chr2:10585164-10591407	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	esv1818042	chr2:10585364-10591407	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	esv1840643	chr2:10585364-10607465	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
11	nsv873649	chr2:10585458-10591628	Weak transcription Flanking Active TSS Enhancers Active TSS 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	37 gene(s)	inside rSNPs	diseases
12	nsv873650	chr2:10585458-10597858	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
13	nsv873651	chr2:10585575-10597858	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
14	esv1792409	chr2:10585687-10588600	Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
15	esv1835530	chr2:10585687-10591407	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10573000-10587400	Weak transcription	Right Atrium	heart
2	chr2:10573800-10586800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:10577200-10587800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:10580000-10587400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:10580000-10587400	Weak transcription	Stomach Mucosa	stomach
6	chr2:10582600-10586600	Weak transcription	Psoas Muscle	Psoas
7	chr2:10582600-10587400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:10584600-10587600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:10584800-10586600	Weak transcription	Aorta	Aorta
10	chr2:10584800-10586600	Weak transcription	NHLF	lung
11	chr2:10584800-10586800	Weak transcription	Brain Substantia Nigra	brain
12	chr2:10584800-10587400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:10584800-10587400	Weak transcription	Pancreas	Pancrea
14	chr2:10585000-10586600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:10585000-10586600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:10585000-10586600	Weak transcription	Brain Angular Gyrus	brain
17	chr2:10585000-10586600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:10585000-10586600	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:10585000-10586800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:10585000-10586800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:10585000-10586800	Weak transcription	Adipose Nuclei	Adipose
22	chr2:10585000-10587200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:10585000-10587400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:10585000-10587400	Weak transcription	Ovary	ovary
25	chr2:10585000-10587400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:10585000-10587400	Weak transcription	Right Ventricle	heart
27	chr2:10585000-10587600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:10585000-10587600	Weak transcription	Esophagus	oesophagus
29	chr2:10585000-10587600	Transcr. at gene 5' and 3'	NHEK	skin
30	chr2:10585000-10587800	Weak transcription	Spleen	Spleen
31	chr2:10585200-10586600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:10585200-10586600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:10585200-10586600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:10585200-10586600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:10585200-10586600	Weak transcription	NHDF-Ad	bronchial
36	chr2:10585200-10586800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr2:10585200-10586800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:10585200-10586800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:10585200-10587000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:10585200-10587200	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr2:10585200-10587400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:10585200-10587400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:10585200-10587400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr2:10585200-10587800	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr2:10585200-10588000	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr2:10585400-10586600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:10585400-10586600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:10585400-10586600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:10585400-10586600	Enhancers	Fetal Brain Male	brain
50	chr2:10585400-10586600	Enhancers	Stomach Smooth Muscle	stomach

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