Variant report

Variant	rs4728163
Chromosome Location	chr7:129054881-129054882
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	chr7:129053794..129056799-chr7:129060226..129064696,5	K562	blood:
2	chr7:129053550..129056799-chr7:129061780..129064830,4	K562	blood:

Variant related genes	Relation type
ENSG00000158467	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1000676	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10248810	0.86[JPT][hapmap]
rs10954226	0.86[JPT][hapmap]
rs10954228	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10954229	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10954230	0.92[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11979476	0.86[JPT][hapmap]
rs12112374	0.86[JPT][hapmap]
rs12534372	0.88[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12540568	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12667132	0.84[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12667232	0.80[CHD][hapmap];0.91[TSI][hapmap]
rs12668958	1.00[ASW][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.96[MKK][hapmap]
rs12671604	0.80[CHD][hapmap];0.91[TSI][hapmap]
rs1526900	0.86[JPT][hapmap]
rs1541711	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1559486	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs17168734	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17168750	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1880854	0.86[JPT][hapmap]
rs2303304	0.85[ASN][1000 genomes]
rs2694572	0.86[JPT][hapmap]
rs2694574	0.84[JPT][hapmap]
rs2718083	0.80[JPT][hapmap]
rs2718084	0.81[JPT][hapmap]
rs34022136	0.91[ASN][1000 genomes]
rs35366945	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35974655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4728162	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4728164	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4731572	0.84[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4731573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4731575	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6467233	0.81[JPT][hapmap]
rs6966595	0.89[CHD][hapmap];0.91[JPT][hapmap]
rs6980385	0.86[JPT][hapmap]
rs753336	0.91[TSI][hapmap]
rs7788327	0.86[JPT][hapmap]
rs822038	0.93[CHD][hapmap];0.91[JPT][hapmap]
rs822040	0.93[CHD][hapmap];0.91[JPT][hapmap]
rs891545	0.81[JPT][hapmap]
rs963465	0.81[JPT][hapmap]
rs9641846	0.81[JPT][hapmap]
rs9641850	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9641851	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs966481	0.80[CHD][hapmap];0.91[TSI][hapmap]
rs974558	0.84[CEU][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516498	chr7:128901429-129072024	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv3331483	chr7:128918442-129082887	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1015550	chr7:128992460-129111060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv539122	chr7:128992460-129111060	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4728163	AHCYL2	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129008400-129073200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr7:129016000-129062400	Weak transcription	Pancreas	Pancrea
3	chr7:129016000-129071400	Weak transcription	Small Intestine	intestine
4	chr7:129016600-129055200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:129017400-129069200	Weak transcription	Stomach Mucosa	stomach
6	chr7:129017400-129073000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr7:129017800-129064600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr7:129018400-129070000	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:129019400-129070800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:129019800-129066200	Weak transcription	Thymus	Thymus
11	chr7:129020000-129064600	Weak transcription	Spleen	Spleen
12	chr7:129026800-129060600	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr7:129027800-129070200	Weak transcription	HepG2	liver
14	chr7:129028400-129063800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:129028400-129073000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:129029000-129070000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:129029200-129073200	Weak transcription	Brain Angular Gyrus	brain
18	chr7:129029600-129067400	Weak transcription	Fetal Brain Male	brain
19	chr7:129033800-129073600	Weak transcription	Right Ventricle	heart
20	chr7:129034200-129066200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:129035600-129062000	Weak transcription	Left Ventricle	heart
22	chr7:129035600-129072600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:129035600-129073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:129040000-129055800	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr7:129041400-129058600	Weak transcription	NHEK	skin
26	chr7:129041400-129066200	Weak transcription	Esophagus	oesophagus
27	chr7:129041400-129067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr7:129041600-129056400	Strong transcription	Liver	Liver
29	chr7:129041600-129064600	Weak transcription	Lung	lung
30	chr7:129041600-129073400	Weak transcription	HMEC	breast
31	chr7:129041800-129063600	Weak transcription	HUVEC	blood vessel
32	chr7:129041800-129066000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:129042000-129055600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr7:129042000-129066000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:129042600-129066200	Weak transcription	Gastric	stomach
36	chr7:129043400-129062600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr7:129043400-129066400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:129043400-129072600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr7:129045000-129063200	Weak transcription	Dnd41	blood
40	chr7:129045600-129063000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:129045800-129055800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:129046600-129062400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr7:129046600-129066200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr7:129046600-129066200	Weak transcription	Aorta	Aorta
45	chr7:129046600-129073400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr7:129047200-129064600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr7:129048000-129062400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr7:129048200-129062400	Weak transcription	Colonic Mucosa	Colon
49	chr7:129048200-129062400	Weak transcription	K562	blood
50	chr7:129048400-129061400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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