Variant report

Variant	rs4612218
Chromosome Location	chr7:65615130-65615131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr7:65614993-65616433	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65610382..65612818-chr7:65612970..65615484,3	K562	blood:

Variant related genes	Relation type
CRCP	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10240249	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10253922	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10256544	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10268656	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10271553	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1129531	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1167390	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1167395	0.81[AMR][1000 genomes]
rs1167399	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1167406	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11971949	0.83[AMR][1000 genomes]
rs13240492	0.82[AMR][1000 genomes]
rs13309935	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1612452	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1616988	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1983372	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2087647	0.82[AMR][1000 genomes]
rs2249458	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2420173	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2420174	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2460430	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2460432	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28391294	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28470208	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2949696	0.81[AMR][1000 genomes]
rs34550048	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35034167	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4368860	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4718319	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4718328	0.81[EUR][1000 genomes]
rs55962648	0.82[AMR][1000 genomes]
rs57866200	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59466412	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62467451	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6946143	0.82[AMR][1000 genomes]
rs6951787	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6957690	0.83[AMR][1000 genomes]
rs6958484	0.82[AMR][1000 genomes]
rs6961717	0.83[AMR][1000 genomes]
rs6967708	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs709608	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs709609	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7782806	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7786892	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7801282	0.82[AMR][1000 genomes]
rs7809814	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs875971	0.82[AMR][1000 genomes]
rs880166	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs908915	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9767916	0.85[AMR][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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs4612218	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs4612218	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs4612218	RP4-756H11.3	cis	Artery Tibial	GTEx
rs4612218	LINC00174	cis	Thyroid	GTEx
rs4612218	GS1-124K5.11	cis	Thyroid	GTEx
rs4612218	GS1-124K5.4	cis	Stomach	GTEx
rs4612218	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4612218	GS1-124K5.2	cis	Whole Blood	GTEx
rs4612218	RP4-756H11.3	cis	Thyroid	GTEx
rs4612218	RNU6-96P	cis	Thyroid	GTEx
rs4612218	GTF2IRD1P1	cis	Thyroid	GTEx
rs4612218	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs4612218	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs4612218	RP4-756H11.3	cis	lung	GTEx
rs4612218	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs4612218	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs4612218	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs4612218	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65581000-65617200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:65595000-65615200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:65595200-65622000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr7:65595600-65623200	Strong transcription	Dnd41	blood
5	chr7:65595600-65623800	Strong transcription	Primary T cells from cord blood	blood
6	chr7:65595800-65617200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr7:65595800-65620000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr7:65599200-65623400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr7:65605800-65615200	Strong transcription	K562	blood
10	chr7:65606600-65617600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:65607400-65617000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:65608200-65617000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:65608400-65615400	Weak transcription	Stomach Mucosa	stomach
14	chr7:65608600-65615600	Weak transcription	HSMMtube	muscle
15	chr7:65609000-65622400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:65609200-65615400	Weak transcription	Fetal Heart	heart
17	chr7:65609200-65615800	Weak transcription	Psoas Muscle	Psoas
18	chr7:65609200-65623200	Weak transcription	Fetal Brain Male	brain
19	chr7:65609200-65623400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:65609600-65624600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr7:65610200-65615800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:65610400-65617000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:65611200-65615400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:65611200-65615400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:65611200-65615600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:65611200-65615600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr7:65611200-65615800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr7:65611200-65617000	Enhancers	NHDF-Ad	bronchial
29	chr7:65611400-65615400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:65611400-65615600	Weak transcription	Ovary	ovary
31	chr7:65611800-65615400	Weak transcription	Primary B cells from cord blood	blood
32	chr7:65612000-65615400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:65612000-65615600	Weak transcription	Brain Angular Gyrus	brain
34	chr7:65612000-65635400	Weak transcription	Fetal Kidney	kidney
35	chr7:65612400-65615400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr7:65612600-65615400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr7:65612600-65615400	Weak transcription	Brain Hippocampus Middle	brain
38	chr7:65612600-65615400	Weak transcription	Colonic Mucosa	Colon
39	chr7:65612600-65615400	Weak transcription	Colon Smooth Muscle	Colon
40	chr7:65612600-65615400	Weak transcription	Esophagus	oesophagus
41	chr7:65612600-65615400	Weak transcription	Right Ventricle	heart
42	chr7:65612600-65615600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:65612600-65617000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr7:65612600-65617000	Weak transcription	Aorta	Aorta
45	chr7:65612800-65615200	Enhancers	Liver	Liver
46	chr7:65612800-65615400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr7:65612800-65615400	Weak transcription	Adipose Nuclei	Adipose
48	chr7:65612800-65615400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr7:65612800-65615600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr7:65612800-65615600	Weak transcription	Gastric	stomach

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