Variant report

Variant	rs55928061
Chromosome Location	chr8:8421412-8421413
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8411447..8415576-chr8:8419918..8422813,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLDN23-1	chr8:8421329-8422570	NONHSAT124878

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10088924	0.85[ASN][1000 genomes]
rs10092416	0.85[ASN][1000 genomes]
rs10109231	0.89[ASN][1000 genomes]
rs11250207	0.86[ASN][1000 genomes]
rs12547686	0.82[ASN][1000 genomes]
rs17154096	0.85[ASN][1000 genomes]
rs17154101	0.88[ASN][1000 genomes]
rs4272382	0.88[ASN][1000 genomes]
rs55646688	0.85[ASN][1000 genomes]
rs59857818	0.88[ASN][1000 genomes]
rs62494866	0.86[ASN][1000 genomes]
rs6601712	0.88[ASN][1000 genomes]
rs73190519	0.97[ASN][1000 genomes]
rs73190522	0.93[ASN][1000 genomes]
rs73662125	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv610153	chr8:8098079-8454531	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1025994	chr8:8108863-8580201	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active 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
5	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription 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	21 gene(s)	inside rSNPs	diseases
7	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv1019613	chr8:8239352-8636357	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
9	nsv539452	chr8:8239352-8636357	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv465452	chr8:8313010-8450761	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv610173	chr8:8313010-8450761	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv465453	chr8:8318850-8439068	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv610174	chr8:8318850-8439068	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv470182	chr8:8318850-8448429	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv465454	chr8:8318850-8448688	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv465455	chr8:8318850-8448688	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv610175	chr8:8318850-8448688	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	nsv465456	chr8:8318850-8450761	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
19	nsv465457	chr8:8318850-8450761	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
20	nsv610176	chr8:8318850-8450761	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
21	nsv610177	chr8:8318850-8454531	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv1026251	chr8:8319925-8448688	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
23	nsv1025433	chr8:8324419-8432339	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv1020159	chr8:8324419-8450231	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv539455	chr8:8324419-8450231	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
26	nsv890333	chr8:8328101-8456563	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
27	nsv890334	chr8:8328101-8471348	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
28	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
29	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
30	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
31	nsv890335	chr8:8394297-8448429	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
32	nsv890336	chr8:8396676-8500562	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
33	nsv6072	chr8:8414563-8440656	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
34	nsv1019794	chr8:8419612-8454162	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8414800-8421600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:8414800-8422000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr8:8419000-8423600	Enhancers	Fetal Lung	lung
4	chr8:8419400-8421600	Weak transcription	NH-A	brain
5	chr8:8419400-8423200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr8:8419600-8421800	Enhancers	Fetal Intestine Large	intestine
7	chr8:8419600-8421800	Weak transcription	Osteobl	bone
8	chr8:8419600-8422000	Weak transcription	A549	lung
9	chr8:8419600-8422400	Enhancers	Fetal Intestine Small	intestine
10	chr8:8420000-8422400	Enhancers	Fetal Stomach	stomach
11	chr8:8420000-8422600	Enhancers	Stomach Mucosa	stomach
12	chr8:8420000-8424600	Enhancers	Ovary	ovary
13	chr8:8420200-8421800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr8:8420200-8422000	Enhancers	Rectal Smooth Muscle	rectum
15	chr8:8420200-8422800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr8:8420200-8423600	Enhancers	Colon Smooth Muscle	Colon
17	chr8:8420200-8423600	Enhancers	Placenta	Placenta
18	chr8:8420200-8424000	Enhancers	Fetal Muscle Leg	muscle
19	chr8:8420400-8422000	Enhancers	Small Intestine	intestine
20	chr8:8420600-8421600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr8:8420600-8421600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr8:8420600-8421600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr8:8420600-8421800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr8:8420800-8423400	Weak transcription	NHLF	lung
25	chr8:8421000-8423000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr8:8421000-8423200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr8:8421200-8421600	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr8:8421200-8422400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr8:8421200-8422600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr8:8421200-8422600	Enhancers	HMEC	breast
31	chr8:8421400-8421800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr8:8421400-8422000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:8421400-8422000	Enhancers	Primary hematopoietic stem cells	blood
34	chr8:8421400-8422200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr8:8421400-8422400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr8:8421400-8422400	Enhancers	Fetal Kidney	kidney
37	chr8:8421400-8422400	Bivalent Enhancer	HepG2	liver
38	chr8:8421400-8422600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr8:8421400-8422600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr8:8421400-8422800	Weak transcription	Brain Germinal Matrix	brain
41	chr8:8421400-8424400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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