Variant report

Variant	rs3823742
Chromosome Location	chr7:39730841-39730842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39729892..39732423-chr7:39733568..39735787,2	K562	blood:
2	chr7:39728943..39730510-chr7:39730672..39733182,2	K562	blood:
3	chr7:39729170..39731392-chr7:39733307..39735068,2	K562	blood:
4	chr7:39723555..39727684-chr7:39728117..39732322,6	K562	blood:
5	chr7:39728709..39730955-chr7:39759969..39761928,2	K562	blood:

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11769865	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11982634	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2107710	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2158548	0.88[EUR][1000 genomes]
rs2158549	0.93[EUR][1000 genomes]
rs2189837	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2237499	0.81[ASN][1000 genomes]
rs2329464	0.93[EUR][1000 genomes]
rs2876862	0.88[EUR][1000 genomes]
rs4723887	0.88[EUR][1000 genomes]
rs4723891	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4723892	0.93[EUR][1000 genomes]
rs6462936	0.83[EUR][1000 genomes]
rs6462937	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6952363	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6952866	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6956681	0.93[EUR][1000 genomes]
rs6961667	0.88[EUR][1000 genomes]
rs6969070	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6969523	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7785049	0.88[EUR][1000 genomes]
rs7806651	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs917077	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv887972	chr7:39666267-39733688	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3823742	LINC00265	cis	Thyroid	GTEx
rs3823742	LINC00265	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39701800-39739400	Weak transcription	Esophagus	oesophagus
2	chr7:39714000-39736800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:39715000-39736600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:39715200-39749400	Weak transcription	Aorta	Aorta
5	chr7:39716800-39735600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:39718200-39739800	Weak transcription	Spleen	Spleen
7	chr7:39721200-39738200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr7:39721400-39735800	Weak transcription	K562	blood
9	chr7:39721800-39736400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:39721800-39736600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:39722000-39737600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:39722800-39738400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:39723000-39731200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:39723200-39736000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr7:39723400-39736800	Weak transcription	Brain Hippocampus Middle	brain
16	chr7:39723600-39742800	Weak transcription	Brain Angular Gyrus	brain
17	chr7:39723800-39736200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr7:39723800-39737000	Weak transcription	Brain Anterior Caudate	brain
19	chr7:39723800-39743000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr7:39724000-39731400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr7:39724000-39739400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:39724200-39736400	Weak transcription	Colonic Mucosa	Colon
23	chr7:39724200-39736600	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:39724200-39741200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr7:39724600-39739000	Weak transcription	Small Intestine	intestine
26	chr7:39725000-39732200	Weak transcription	Fetal Heart	heart
27	chr7:39725400-39732000	Genic enhancers	HUVEC	blood vessel
28	chr7:39726400-39736800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:39726400-39737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr7:39726600-39733400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:39726600-39742800	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr7:39727000-39731600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:39727000-39732400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:39727000-39733400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr7:39727000-39733600	Strong transcription	Fetal Lung	lung
36	chr7:39727000-39734200	Strong transcription	Primary T cells from cord blood	blood
37	chr7:39727000-39738000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr7:39727200-39732200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:39727200-39732800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr7:39727200-39732800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr7:39727200-39732800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:39727200-39733800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr7:39727400-39731800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr7:39727400-39733400	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr7:39727400-39733400	Strong transcription	Fetal Intestine Large	intestine
46	chr7:39727400-39741600	Strong transcription	Fetal Muscle Leg	muscle
47	chr7:39727400-39747800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr7:39727600-39731600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr7:39727600-39732400	Strong transcription	Fetal Thymus	thymus
50	chr7:39727600-39734400	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links