Variant report

Variant	rs11936560
Chromosome Location	chr4:20704538-20704539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:20701257..20703146-chr4:20703451..20705273,2	MCF-7	breast:
2	chr4:20702888..20705883-chr4:20707634..20710929,3	K562	blood:
3	chr4:20702290..20704847-chr4:20728043..20731005,3	K562	blood:

Variant related genes	Relation type
ENSG00000163138	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10031524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938803	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11940062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1820505	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114474	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2322687	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3764965	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs3816874	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4577580	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55874299	0.81[EUR][1000 genomes]
rs61428210	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6447971	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447972	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447973	0.82[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6811933	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6857386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6858843	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7662488	0.81[ASN][1000 genomes]
rs7663837	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7668797	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689421	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7694208	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs964019	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS 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	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11936560	C4orf28	Cis_1M	lymphoblastoid	RTeQTL
rs11936560	PACRGL	cis	Thyroid	GTEx
rs11936560	PACRGL	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20702400-20722600	Weak transcription	Spleen	Spleen
2	chr4:20702600-20706000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:20702600-20706200	Weak transcription	Lung	lung
4	chr4:20702600-20717200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:20702800-20706000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:20702800-20706200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:20702800-20707400	Weak transcription	Aorta	Aorta
8	chr4:20703000-20706000	Weak transcription	Primary T cells from cord blood	blood
9	chr4:20703000-20706000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:20703000-20706000	Weak transcription	HSMMtube	muscle
11	chr4:20703000-20706200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:20703000-20706200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:20703000-20706200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:20703000-20706200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:20703000-20706200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:20703000-20706200	Weak transcription	Brain Substantia Nigra	brain
17	chr4:20703000-20706200	Weak transcription	Colonic Mucosa	Colon
18	chr4:20703000-20706200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:20703000-20706200	Weak transcription	Esophagus	oesophagus
20	chr4:20703000-20706200	Weak transcription	Fetal Kidney	kidney
21	chr4:20703000-20706200	Weak transcription	Placenta	Placenta
22	chr4:20703000-20706200	Weak transcription	Fetal Thymus	thymus
23	chr4:20703000-20706200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:20703000-20706200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr4:20703000-20706400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:20703000-20706400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:20703000-20706400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr4:20703000-20706600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:20703000-20706600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:20703000-20707000	Weak transcription	Thymus	Thymus
31	chr4:20703000-20708600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:20703000-20717200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:20703000-20717400	Weak transcription	Fetal Heart	heart
34	chr4:20703000-20721800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:20703000-20722800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:20703000-20741400	Weak transcription	Stomach Mucosa	stomach
37	chr4:20703200-20705600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:20703200-20705600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:20703200-20706000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr4:20703200-20706000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:20703200-20706200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:20703200-20706200	Weak transcription	Primary B cells from cord blood	blood
43	chr4:20703200-20706200	Weak transcription	Adipose Nuclei	Adipose
44	chr4:20703200-20706200	Weak transcription	Right Ventricle	heart
45	chr4:20703200-20706200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr4:20703200-20706200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr4:20703200-20706200	Weak transcription	NH-A	brain
48	chr4:20703200-20706400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr4:20703200-20706400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:20703200-20706400	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links