Variant report

Variant	rs2156638
Chromosome Location	chr11:57542998-57542999
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57506998..57509291-chr11:57540443..57545321,4	K562	blood:
2	chr11:57541504..57544488-chr11:62607869..62609390,2	MCF-7	breast:
3	chr11:57527377..57534826-chr11:57541861..57548775,13	MCF-7	breast:
4	chr11:57540282..57543092-chr11:57543604..57545694,2	K562	blood:
5	chr11:57540348..57543144-chr11:57545793..57547381,2	K562	blood:
6	chr11:57529498..57532508-chr11:57541660..57544888,3	K562	blood:
7	chr11:57542706..57545310-chr11:57561763..57564745,3	MCF-7	breast:
8	chr11:57533309..57536452-chr11:57541142..57544188,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198561	Chromatin interaction
ENSG00000211450	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10750870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10792110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896644	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10896649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10896653	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229109	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229119	0.88[AMR][1000 genomes]
rs11570176	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11570181	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12270209	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12274865	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12363024	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12805343	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1424753	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613592	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1624389	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1631684	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1647394	0.82[ASN][1000 genomes]
rs1647403	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs17455422	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17455626	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783818	0.89[CEU][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783824	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783826	0.89[JPT][hapmap]
rs1783827	0.89[JPT][hapmap]
rs1783828	1.00[JPT][hapmap]
rs1783976	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783977	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1783978	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783979	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783980	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783981	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783983	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs1783985	0.85[ASN][1000 genomes]
rs1785498	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1785499	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1786438	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1798172	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1798173	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1798177	1.00[JPT][hapmap]
rs2911728	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2956981	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2956982	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3017889	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36036499	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471398	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs547118	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56392705	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs585337	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs585761	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs588612	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs593239	0.81[ASN][1000 genomes]
rs606499	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs623541	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs627145	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs639158	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs644219	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs645145	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs652191	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs652908	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs653889	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs658936	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs659165	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs665058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs666021	0.88[JPT][hapmap]
rs671508	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs682258	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs686489	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7105506	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115528	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7117020	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7120868	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7479922	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947357	1.00[JPT][hapmap]
rs7948571	0.93[ASN][1000 genomes]
rs929934	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv327	chr11:57532641-57550746	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2156638	YPEL4	cis	lung	GTEx
rs2156638	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2156638	ZDHHC5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57530400-57545800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr11:57531400-57543200	Weak transcription	Primary B cells from cord blood	blood
3	chr11:57531800-57543200	Weak transcription	Thymus	Thymus
4	chr11:57532800-57543200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:57533400-57543000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:57535200-57543000	Weak transcription	Fetal Brain Female	brain
7	chr11:57538400-57546000	Enhancers	Small Intestine	intestine
8	chr11:57538400-57549800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:57538600-57543000	Weak transcription	Fetal Thymus	thymus
10	chr11:57538600-57543200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr11:57538600-57543400	Weak transcription	Primary T cells from cord blood	blood
12	chr11:57538600-57545000	Enhancers	Liver	Liver
13	chr11:57539200-57543400	Weak transcription	Aorta	Aorta
14	chr11:57539200-57543400	Enhancers	Left Ventricle	heart
15	chr11:57539200-57544000	Enhancers	HepG2	liver
16	chr11:57539600-57543200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr11:57539600-57552000	Enhancers	Placenta	Placenta
18	chr11:57539800-57543000	Enhancers	Brain Hippocampus Middle	brain
19	chr11:57539800-57543200	Enhancers	Fetal Heart	heart
20	chr11:57540200-57543800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr11:57540200-57545600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr11:57540400-57544800	Weak transcription	Gastric	stomach
23	chr11:57540600-57543200	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr11:57541000-57543000	Weak transcription	Pancreas	Pancrea
25	chr11:57541200-57545200	Enhancers	Stomach Mucosa	stomach
26	chr11:57541200-57545400	Enhancers	Right Ventricle	heart
27	chr11:57541400-57543000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:57541400-57543000	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr11:57541400-57543200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:57541400-57543600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:57541400-57543600	Weak transcription	Lung	lung
32	chr11:57541600-57543000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr11:57541600-57543000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:57541600-57543000	Enhancers	Duodenum Mucosa	Duodenum
35	chr11:57541600-57543000	Enhancers	Fetal Lung	lung
36	chr11:57541600-57543000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr11:57541600-57543200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr11:57541600-57543200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr11:57541600-57543600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr11:57541600-57545600	Enhancers	Fetal Intestine Small	intestine
41	chr11:57541600-57545800	Enhancers	Brain Angular Gyrus	brain
42	chr11:57541600-57550400	Enhancers	Placenta Amnion	Placenta Amnion
43	chr11:57541800-57544400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr11:57541800-57545400	Enhancers	Colonic Mucosa	Colon
45	chr11:57541800-57545600	Enhancers	Spleen	Spleen
46	chr11:57541800-57545800	Enhancers	H9 Cell Line	embryonic stem cell
47	chr11:57541800-57549000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:57542000-57543000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:57542000-57545400	Enhancers	Fetal Stomach	stomach
50	chr11:57542200-57543000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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