Variant report

Variant	rs10462510
Chromosome Location	chr5:74319745-74319746
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GCNT4-1	chr5:74319656-74319753	ENSG00000249856.1

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11955513	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12515891	0.96[ASN][1000 genomes]
rs12657763	0.80[EUR][1000 genomes]
rs4492095	0.89[ASN][1000 genomes]
rs4704166	0.89[ASN][1000 genomes]
rs58243356	0.86[ASN][1000 genomes]
rs58323964	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59992473	0.85[ASN][1000 genomes]
rs60661930	0.84[ASN][1000 genomes]
rs61342638	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61616736	0.85[ASN][1000 genomes]
rs62369187	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62369188	0.90[ASN][1000 genomes]
rs72768303	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72768311	0.86[ASN][1000 genomes]
rs7706858	0.89[ASN][1000 genomes]
rs7734055	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7736471	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830352	chr5:74189495-74337944	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1018865	chr5:74246293-74494552	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv969994	chr5:74314591-74330479	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr5:74313600-74341800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:74314600-74324800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:74315200-74320400	Enhancers	Stomach Mucosa	stomach
4	chr5:74315200-74332800	Weak transcription	NHDF-Ad	bronchial
5	chr5:74316200-74324200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:74316400-74328000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:74316400-74328200	Weak transcription	Placenta	Placenta
8	chr5:74316400-74330200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:74317200-74331400	Weak transcription	Fetal Intestine Large	intestine
10	chr5:74317400-74323800	Weak transcription	Gastric	stomach
11	chr5:74317400-74326800	Weak transcription	Fetal Intestine Small	intestine
12	chr5:74317600-74344200	Weak transcription	Ovary	ovary
13	chr5:74317800-74332600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:74318400-74320600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr5:74318400-74320600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr5:74318600-74320400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr5:74318600-74320600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr5:74318800-74319800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:74318800-74320000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr5:74318800-74320600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:74319000-74320800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:74319200-74320200	Enhancers	Primary T cells from cord blood	blood
23	chr5:74319200-74320400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr5:74319200-74320400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:74319400-74320200	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr5:74319600-74319800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:74319600-74319800	Enhancers	Pancreas	Pancrea
28	chr5:74319600-74320000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr5:74319600-74320200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:74319600-74320400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:74319600-74320600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:74319600-74320600	Enhancers	Primary T cells fromperipheralblood	blood
33	chr5:74319600-74320600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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