Variant report

Variant	rs4277334
Chromosome Location	chr16:70520028-70520029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:70510922..70516361-chr16:70517334..70521909,5	K562	blood:
2	chr16:70518786..70520618-chr16:70554933..70557035,2	K562	blood:

Variant related genes	Relation type
ENSG00000157353	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11075767	0.81[EUR][1000 genomes]
rs11075768	0.81[EUR][1000 genomes]
rs11075770	0.81[EUR][1000 genomes]
rs11641683	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11645437	0.81[EUR][1000 genomes]
rs11645585	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11648402	0.81[EUR][1000 genomes]
rs11649624	0.81[EUR][1000 genomes]
rs11866400	0.83[EUR][1000 genomes]
rs12597401	0.80[EUR][1000 genomes]
rs12925729	0.81[EUR][1000 genomes]
rs12933634	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288491	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303792	0.89[ASN][1000 genomes]
rs2303793	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33910368	0.82[EUR][1000 genomes]
rs34567847	0.81[EUR][1000 genomes]
rs34890962	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3762171	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4324119	0.80[EUR][1000 genomes]
rs4436771	0.81[EUR][1000 genomes]
rs4513092	0.81[EUR][1000 genomes]
rs4592653	0.80[EUR][1000 genomes]
rs58963621	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6499320	0.80[EUR][1000 genomes]
rs6499321	0.80[EUR][1000 genomes]
rs7194521	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7197262	0.81[EUR][1000 genomes]
rs7199859	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7200430	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7201750	0.81[EUR][1000 genomes]
rs7204583	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs722579	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8045651	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8046881	0.83[EUR][1000 genomes]
rs8049641	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8049786	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8051506	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8052125	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8057610	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8063990	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8064013	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9635522	0.81[EUR][1000 genomes]
rs9929904	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9936225	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv2830027	chr16:70473934-70558039	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4277334	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs4277334	RP11-296I10.6	cis	Artery Tibial	GTEx
rs4277334	CLEC18A	cis	Whole Blood	GTEx
rs4277334	RP11-296I10.6	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70489400-70556400	Weak transcription	Stomach Mucosa	stomach
2	chr16:70501200-70535800	Strong transcription	Fetal Intestine Small	intestine
3	chr16:70501400-70535200	Strong transcription	Fetal Intestine Large	intestine
4	chr16:70501400-70536400	Strong transcription	Fetal Stomach	stomach
5	chr16:70503800-70522200	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr16:70504200-70524800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr16:70504200-70532000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr16:70504400-70535200	Strong transcription	Liver	Liver
9	chr16:70506200-70524000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr16:70506400-70535200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr16:70506600-70522800	Weak transcription	Fetal Brain Male	brain
12	chr16:70506600-70535400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr16:70507000-70520400	Strong transcription	Brain Anterior Caudate	brain
14	chr16:70511000-70527400	Weak transcription	Psoas Muscle	Psoas
15	chr16:70511400-70526200	Strong transcription	Thymus	Thymus
16	chr16:70511600-70524200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr16:70511800-70524800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:70511800-70535600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr16:70512000-70524600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr16:70512000-70535400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr16:70512200-70520600	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr16:70512200-70521200	Strong transcription	Fetal Thymus	thymus
23	chr16:70512800-70524200	Strong transcription	Fetal Muscle Leg	muscle
24	chr16:70512800-70533600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr16:70512800-70556400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr16:70513000-70528000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr16:70513000-70528600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr16:70513200-70522000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr16:70513600-70522600	Strong transcription	Adipose Nuclei	Adipose
30	chr16:70513600-70527600	Weak transcription	Right Atrium	heart
31	chr16:70513800-70520800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr16:70513800-70532200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr16:70514000-70520600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr16:70514000-70523400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr16:70514000-70524400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr16:70514200-70520400	Strong transcription	Lung	lung
37	chr16:70514400-70524800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr16:70514400-70527800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr16:70514600-70523400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr16:70514800-70524200	Weak transcription	Fetal Heart	heart
41	chr16:70515800-70524000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr16:70516000-70530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr16:70516200-70527200	Weak transcription	Small Intestine	intestine
44	chr16:70516600-70520400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr16:70516800-70521800	Strong transcription	Placenta	Placenta
46	chr16:70516800-70522200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr16:70516800-70522200	Weak transcription	Hela-S3	cervix
48	chr16:70516800-70523600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr16:70516800-70527000	Weak transcription	A549	lung
50	chr16:70516800-70527400	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links