Variant report

Variant	rs10758688
Chromosome Location	chr9:5429721-5429722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27839305..27840965-chr9:5427967..5430653,2	MCF-7	breast:
2	chr9:5428095..5431917-chr9:5434732..5438237,4	MCF-7	breast:
3	chr9:5426243..5430131-chr9:5436260..5438892,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RLN1-2	chr9:5429450-5431224	NONHSAT130101

Variant related genes	Relation type
ENSG00000182572	Chromatin interaction
ENSG00000107020	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10739074	0.83[EUR][1000 genomes]
rs10739075	0.93[EUR][1000 genomes]
rs10758689	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10815221	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815223	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10975112	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975113	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10975114	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10975116	0.86[EUR][1000 genomes]
rs1322250	0.84[EUR][1000 genomes]
rs2093455	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2093456	0.91[EUR][1000 genomes]
rs2295870	0.92[EUR][1000 genomes]
rs3780392	0.84[EUR][1000 genomes]
rs4742092	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7023253	0.91[EUR][1000 genomes]
rs7862054	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892136	chr9:4921639-5436461	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv529689	chr9:4970093-5483250	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv892141	chr9:5116616-5479822	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1017126	chr9:5117847-5695486	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv539964	chr9:5117847-5695486	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv949627	chr9:5174829-5712626	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv427837	chr9:5189756-5454512	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers 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	25 gene(s)	inside rSNPs	diseases
8	esv2759660	chr9:5288908-5454512	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv2758177	chr9:5297921-5454512	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv466108	chr9:5345673-5514372	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
11	nsv613196	chr9:5345673-5514372	Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer 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	18 gene(s)	inside rSNPs	diseases
12	esv3330820	chr9:5366750-5510260	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5376000-5436800	Weak transcription	Psoas Muscle	Psoas
2	chr9:5408800-5435400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:5409000-5430000	Weak transcription	Liver	Liver
4	chr9:5409800-5436400	Weak transcription	Small Intestine	intestine
5	chr9:5410000-5430200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr9:5410000-5435400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:5410000-5435400	Weak transcription	Dnd41	blood
8	chr9:5413000-5430600	Weak transcription	HSMM	muscle
9	chr9:5415400-5437000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:5416800-5435400	Weak transcription	Fetal Lung	lung
11	chr9:5417200-5430000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:5418000-5434200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:5418200-5432000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:5418400-5436600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr9:5418600-5432200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:5418800-5433200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr9:5419000-5430000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:5419000-5430200	Weak transcription	GM12878-XiMat	blood
19	chr9:5419000-5430600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:5419000-5432400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:5419000-5432800	Weak transcription	Esophagus	oesophagus
22	chr9:5419000-5435400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr9:5419000-5435400	Weak transcription	HSMMtube	muscle
24	chr9:5419200-5430600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr9:5419200-5432400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:5419200-5432600	Weak transcription	Fetal Stomach	stomach
27	chr9:5419200-5433000	Weak transcription	Ovary	ovary
28	chr9:5419200-5433200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr9:5419200-5433400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:5419200-5435400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:5419200-5437000	Weak transcription	Aorta	Aorta
32	chr9:5419200-5437000	Weak transcription	Pancreas	Pancrea
33	chr9:5419400-5429800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr9:5419400-5432000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:5419400-5432400	Weak transcription	Brain Germinal Matrix	brain
36	chr9:5419400-5432600	Weak transcription	Spleen	Spleen
37	chr9:5419600-5430000	Weak transcription	Lung	lung
38	chr9:5419600-5432400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr9:5419600-5432400	Weak transcription	Fetal Intestine Large	intestine
40	chr9:5419600-5435400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:5420000-5436800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr9:5421600-5430000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr9:5423600-5429800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:5423600-5435600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr9:5424800-5432200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr9:5425000-5435600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr9:5425200-5435600	Weak transcription	Fetal Heart	heart
48	chr9:5425400-5435800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr9:5425600-5435400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:5426000-5433800	Strong transcription	Primary T cells from cord blood	blood

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