Variant report

Variant	rs4237145
Chromosome Location	chr9:2493123-2493124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2486399..2488878-chr9:2490772..2493168,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA0020-1	chr9:2493075-2493180	ENSG00000236404.4
2	lnc-KIAA0020-1	chr9:2493073-2493180	ENSG00000236404

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10738699	1.00[ASN][1000 genomes]
rs10757489	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10757500	1.00[ASN][1000 genomes]
rs10966539	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967100	1.00[CHD][hapmap]
rs11790050	1.00[ASN][1000 genomes]
rs12348301	1.00[CHD][hapmap]
rs1331465	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473839	1.00[CHD][hapmap]
rs1512713	1.00[CHD][hapmap]
rs1571813	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571816	1.00[ASN][1000 genomes]
rs16906913	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656045	1.00[CHD][hapmap]
rs1854878	1.00[ASN][1000 genomes]
rs1929468	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168136	1.00[CHD][hapmap]
rs2183735	1.00[ASN][1000 genomes]
rs2376106	1.00[ASN][1000 genomes]
rs2889291	1.00[ASN][1000 genomes]
rs7036544	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042212	1.00[ASN][1000 genomes]
rs7043199	1.00[ASN][1000 genomes]
rs7858086	1.00[CHD][hapmap]
rs7864004	1.00[CHD][hapmap]

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	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
2	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
3	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv531563	chr9:2324333-2501030	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1021309	chr9:2336185-2506959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv466081	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv613132	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv892066	chr9:2397564-2589739	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1020479	chr9:2407980-2528346	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv539933	chr9:2407980-2528346	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv892067	chr9:2416895-2515607	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2476200-2493600	Weak transcription	Fetal Brain Female	brain
2	chr9:2484800-2493600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:2487400-2493200	Weak transcription	Brain Angular Gyrus	brain
4	chr9:2487400-2493200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr9:2487400-2495000	Weak transcription	Right Ventricle	heart
6	chr9:2487400-2533400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:2487600-2493400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:2488400-2495600	Weak transcription	Right Atrium	heart
9	chr9:2488600-2494400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:2488600-2494400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:2490400-2494400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:2490400-2494800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:2490600-2493400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:2491000-2494400	Weak transcription	Fetal Muscle Leg	muscle
15	chr9:2491400-2494000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr9:2491400-2495600	Weak transcription	Left Ventricle	heart
17	chr9:2492600-2493200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:2492600-2494800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:2492600-2494800	Enhancers	Ovary	ovary
20	chr9:2492800-2493200	Enhancers	Rectal Smooth Muscle	rectum
21	chr9:2492800-2493600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr9:2492800-2495000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr9:2493000-2493400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr9:2493000-2493600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr9:2493000-2493800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:2493000-2494000	Enhancers	Psoas Muscle	Psoas
27	chr9:2493000-2494600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:2493000-2494800	Enhancers	Fetal Stomach	stomach
29	chr9:2493000-2496000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:2493000-2496400	Enhancers	Fetal Heart	heart
31	chr9:2493000-2496800	Enhancers	Fetal Lung	lung
32	chr9:2493000-2496800	Enhancers	Stomach Smooth Muscle	stomach
33	chr9:2493000-2498000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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