Variant report

Variant	rs10964458
Chromosome Location	chr9:2027576-2027577
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	POLR2A	chr9:2027521-2028407	GM12891	blood:	n/a	n/a
2	POLR2A	chr9:2027497-2028430	GM12892	blood:	n/a	n/a
3	POLR2A	chr9:2027478-2028141	GM12891	blood:	n/a	n/a
4	SIN3AK20	chr9:2027463-2028367	MCF-7	breast:	n/a	n/a
5	POLR2A	chr9:2027509-2028432	GM12892	blood:	n/a	n/a
6	POLR2A	chr9:2027485-2027985	GM12892	blood:	n/a	n/a
7	POLR2A	chr9:2027553-2027767	GM12878	blood:	n/a	n/a
8	POLR2A	chr9:2027466-2028485	GM12892	blood:	n/a	n/a
9	POLR2A	chr9:2027470-2028453	GM12878	blood:	n/a	n/a
10	POLR2A	chr9:2027566-2027614	MCF-7	breast:	n/a	n/a
11	POLR2A	chr9:2026705-2028628	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2027542..2030484-chr9:2031269..2033941,3	K562	blood:
2	chr9:2014683..2019202-chr9:2026620..2030174,6	MCF-7	breast:

Variant related genes	Relation type
SMARCA2	TF binding region
ENSG00000080503	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10757122	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10964457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10964461	0.84[CEU][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10964465	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10964466	0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10964471	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs10964507	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1021712	chr9:1647840-2216839	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic 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 miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv539921	chr9:1647840-2216839	Bivalent Enhancer Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv831493	chr9:1885733-2074135	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv892048	chr9:1888703-2177391	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1021158	chr9:1963930-2040728	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
9	nsv892052	chr9:1980819-2072470	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv2830420	chr9:1998911-2119702	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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	9 gene(s)	inside rSNPs	diseases
11	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv613079	chr9:2012767-2059341	Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv466069	chr9:2018825-2066493	Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv613080	chr9:2018825-2066493	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv466070	chr9:2024639-2044721	Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv613081	chr9:2024639-2044721	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv892053	chr9:2024639-2062014	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2018000-2028200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:2018200-2033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:2019000-2032800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:2019000-2033200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:2019200-2032600	Weak transcription	A549	lung
6	chr9:2019200-2039400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:2019400-2027600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:2019400-2030000	Enhancers	Adipose Nuclei	Adipose
9	chr9:2019400-2030400	Enhancers	Colon Smooth Muscle	Colon
10	chr9:2019400-2030800	Weak transcription	NHDF-Ad	bronchial
11	chr9:2019400-2032800	Weak transcription	Osteobl	bone
12	chr9:2019400-2033000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:2019400-2033200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:2020000-2033000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:2020400-2028800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:2021400-2028400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr9:2021600-2028200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr9:2022000-2032200	Weak transcription	NHEK	skin
19	chr9:2022200-2028600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr9:2022200-2029600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr9:2022400-2028200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr9:2022800-2029200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr9:2023000-2027800	Weak transcription	HMEC	breast
24	chr9:2023200-2030600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr9:2023200-2032400	Weak transcription	Fetal Kidney	kidney
26	chr9:2023400-2027600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr9:2023400-2027800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:2023400-2028000	Weak transcription	Fetal Brain Male	brain
29	chr9:2023400-2029400	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr9:2023400-2029800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr9:2023400-2030000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr9:2023600-2031000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr9:2023600-2033000	Weak transcription	Fetal Brain Female	brain
34	chr9:2023800-2027600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:2023800-2029600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr9:2023800-2029600	Enhancers	Brain Anterior Caudate	brain
37	chr9:2023800-2032400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr9:2024000-2027800	Weak transcription	Fetal Lung	lung
39	chr9:2024000-2039400	Weak transcription	Stomach Mucosa	stomach
40	chr9:2024400-2028600	Enhancers	Placenta	Placenta
41	chr9:2024600-2029200	Enhancers	Primary T cells from cord blood	blood
42	chr9:2024800-2027600	Weak transcription	Brain Germinal Matrix	brain
43	chr9:2024800-2028600	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr9:2024800-2032400	Weak transcription	Hela-S3	cervix
45	chr9:2025000-2029800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:2025000-2033000	Weak transcription	HSMMtube	muscle
47	chr9:2025200-2027600	Weak transcription	Gastric	stomach
48	chr9:2025200-2028400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:2025200-2033000	Weak transcription	Thymus	Thymus
50	chr9:2025200-2044600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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