Variant report

Variant	rs945189
Chromosome Location	chr10:99091766-99091767
allele	C/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	chr10:99091645-99092141	Hela-S3	cervix:	n/a	n/a
2	ESRRA	chr10:99091641-99094073	GM12878	blood:	n/a	n/a
3	CHD1	chr10:99091626-99095332	IMR90	lung:	n/a	chr10:99094876-99094886
4	POLR2A	chr10:99091696-99092037	K562	blood:	n/a	n/a
5	POLR2A	chr10:99091605-99092063	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr10:99090879-99092231	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF263	chr10:99091698-99091978	HEK293-T-REx	kidney:	n/a	chr10:99091736-99091745
8	POLR2A	chr10:99091687-99093824	HepG2	liver:	n/a	n/a
9	POLR2A	chr10:99091615-99091963	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr10:99091657-99091969	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:99089670..99092667-chr10:99113757..99116464,3	MCF-7	breast:
2	chr10:99050912..99053751-chr10:99091766..99095025,5	MCF-7	breast:
3	chr10:99090785..99094308-chr10:99157737..99162145,4	MCF-7	breast:
4	chr10:99091261..99093952-chr10:99104801..99106882,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225850	TF binding region
ENSG00000231970	Chromatin interaction
ENSG00000269891	Chromatin interaction
ENSG00000213390	Chromatin interaction
ENSG00000052749	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10736115	0.87[CEU][hapmap]
rs10748691	0.96[CEU][hapmap]
rs10748694	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs10786321	0.87[CEU][hapmap]
rs10786326	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10786327	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10786329	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10786330	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786332	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786333	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786334	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10786335	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882881	0.96[CEU][hapmap]
rs10882883	1.00[CEU][hapmap]
rs10882884	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs10882889	0.91[CEU][hapmap]
rs10882891	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.88[ASN][1000 genomes]
rs10882894	0.84[ASN][1000 genomes]
rs10882895	0.81[ASN][1000 genomes]
rs10882897	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882898	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882899	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189120	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189122	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189127	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189137	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189138	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12221430	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12413688	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12571098	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1334892	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1468069	0.91[CEU][hapmap]
rs1890966	0.99[ASN][1000 genomes]
rs2065861	0.86[CEU][hapmap]
rs2297987	0.91[CEU][hapmap]
rs2861875	0.96[CEU][hapmap]
rs3740512	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3740522	0.96[CEU][hapmap];0.80[JPT][hapmap]
rs3781373	0.91[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3814164	0.96[CEU][hapmap]
rs4917766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4919087	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4919089	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4919090	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4919091	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61863767	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6584116	0.87[ASN][1000 genomes]
rs7067835	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7076523	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7078288	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7080275	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7901853	0.87[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs945187	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
3	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv831952	chr10:98998344-99145924	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv895914	chr10:99006083-99131676	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv825533	chr10:99070570-99115599	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv825534	chr10:99081505-99115599	Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 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	chr10:99081200-99092600	Weak transcription	Aorta	Aorta
2	chr10:99081800-99091800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr10:99081800-99092000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr10:99081800-99092600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:99085200-99091800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr10:99086800-99091800	Enhancers	Pancreas	Pancrea
7	chr10:99086800-99093200	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
8	chr10:99087600-99091800	Enhancers	Right Ventricle	heart
9	chr10:99088000-99091800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr10:99088400-99093400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
11	chr10:99089000-99091800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr10:99089000-99092400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr10:99089200-99092400	Weak transcription	GM12878-XiMat	blood
14	chr10:99089400-99092000	Enhancers	Left Ventricle	heart
15	chr10:99089800-99091800	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr10:99089800-99092200	Enhancers	Gastric	stomach
17	chr10:99090000-99092000	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
18	chr10:99090000-99092400	Genic enhancers	Primary B cells from peripheral blood	blood
19	chr10:99090200-99091800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr10:99090600-99092600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr10:99090800-99091800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr10:99090800-99091800	Enhancers	Fetal Brain Male	brain
23	chr10:99090800-99091800	Enhancers	Fetal Heart	heart
24	chr10:99090800-99091800	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr10:99090800-99092000	Enhancers	Spleen	Spleen
26	chr10:99090800-99092400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr10:99090800-99095000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr10:99091000-99091800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr10:99091000-99091800	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr10:99091000-99091800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr10:99091000-99091800	Enhancers	Ovary	ovary
32	chr10:99091000-99091800	Enhancers	NHDF-Ad	bronchial
33	chr10:99091000-99091800	Enhancers	NHEK	skin
34	chr10:99091000-99092000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr10:99091000-99092200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
36	chr10:99091000-99092200	Enhancers	Brain Substantia Nigra	brain
37	chr10:99091000-99092200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr10:99091000-99092200	Flanking Active TSS	Hela-S3	cervix
39	chr10:99091000-99092400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr10:99091000-99092400	Enhancers	Dnd41	blood
41	chr10:99091000-99092600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr10:99091000-99092600	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
43	chr10:99091000-99092600	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr10:99091000-99092800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr10:99091000-99092800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr10:99091200-99091800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr10:99091200-99091800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr10:99091200-99091800	Enhancers	Brain Hippocampus Middle	brain
49	chr10:99091200-99091800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr10:99091200-99091800	Enhancers	Small Intestine	intestine

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