Variant report

Variant	rs907652
Chromosome Location	chr5:9549178-9549179
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCT5-4	chr5:9549102-9549702	ENSG00000250786
2	lnc-CCT5-4	chr5:9549102-9549261	ENSG00000250786
3	lnc-CCT5-4	chr5:9549102-9549299	NONHSAT100369
4	lnc-CCT5-4	chr5:9548191-9550410	NONHSAT100370
5	lnc-CCT5-4	chr5:9549102-9549261	NR_045196

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12055364	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12186736	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16883128	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs17263889	0.93[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs17329702	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2271220	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3798085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3798098	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6555607	0.91[ASN][1000 genomes]
rs6872486	0.90[ASN][1000 genomes]
rs72731105	0.91[ASN][1000 genomes]
rs7714356	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv597073	chr5:9533854-9550642	Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv1023329	chr5:9543307-9731720	Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9547000-9554200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:9548000-9549400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:9548000-9549800	Weak transcription	Gastric	stomach
4	chr5:9548000-9551400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:9548200-9549200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:9548200-9549200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:9548200-9549400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:9548200-9549400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:9548200-9549400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:9548200-9549400	Weak transcription	Adipose Nuclei	Adipose
11	chr5:9548200-9549400	Weak transcription	Aorta	Aorta
12	chr5:9548200-9549400	Weak transcription	Brain Substantia Nigra	brain
13	chr5:9548200-9549400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:9548200-9549600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:9548200-9549600	Weak transcription	Esophagus	oesophagus
16	chr5:9548200-9549600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:9548200-9549600	Weak transcription	Fetal Intestine Small	intestine
18	chr5:9548200-9549600	Weak transcription	Lung	lung
19	chr5:9548200-9549600	Weak transcription	Pancreas	Pancrea
20	chr5:9548200-9549800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:9548200-9551000	Weak transcription	Ovary	ovary
22	chr5:9548200-9551800	Weak transcription	Brain Anterior Caudate	brain
23	chr5:9548200-9552400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:9548200-9552800	Weak transcription	Stomach Mucosa	stomach
25	chr5:9548200-9553000	Weak transcription	Fetal Kidney	kidney
26	chr5:9548200-9554000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:9548200-9554200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr5:9548200-9556200	Weak transcription	Right Ventricle	heart
29	chr5:9548200-9558400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr5:9548200-9558400	Weak transcription	Liver	Liver
31	chr5:9548400-9549200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:9548400-9549200	Transcr. at gene 5' and 3'	Osteobl	bone
33	chr5:9548400-9549400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:9548400-9549600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:9548400-9553600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr5:9548400-9558400	Weak transcription	Fetal Heart	heart
37	chr5:9548600-9549200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr5:9548600-9549200	Genic enhancers	Rectal Mucosa Donor 31	rectum
39	chr5:9548600-9552800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:9548600-9558400	Weak transcription	Brain Hippocampus Middle	brain
41	chr5:9548800-9549200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:9548800-9549200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:9548800-9549200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:9548800-9549200	Weak transcription	Fetal Lung	lung
45	chr5:9548800-9549200	Transcr. at gene 5' and 3'	NH-A	brain
46	chr5:9548800-9549400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:9548800-9549400	Weak transcription	HMEC	breast
48	chr5:9548800-9549400	Genic enhancers	NHLF	lung
49	chr5:9548800-9549600	Enhancers	Placenta Amnion	Placenta Amnion
50	chr5:9548800-9550000	Genic enhancers	NHDF-Ad	bronchial

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