Variant report

Variant	rs4930390
Chromosome Location	chr11:66560023-66560024
allele	A/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	chr11:66510242..66514990-chr11:66554599..66560135,5	MCF-7	breast:
2	chr11:66137431..66139423-chr11:66559260..66561220,2	MCF-7	breast:
3	chr11:66494295..66496502-chr11:66557467..66560536,4	MCF-7	breast:
4	chr11:66505646..66507981-chr11:66558837..66561189,2	K562	blood:
5	chr11:66558348..66560113-chr11:66560242..66561873,2	MCF-7	breast:
6	chr11:66515358..66517711-chr11:66557412..66560758,4	MCF-7	breast:
7	chr11:66510377..66514075-chr11:66555524..66560274,6	MCF-7	breast:
8	chr11:66502009..66503627-chr11:66558147..66560274,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173715	Chromatin interaction
ENSG00000173898	Chromatin interaction
ENSG00000174669	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10160758	0.85[ASW][hapmap];0.86[CEU][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs10750790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10791889	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs10791890	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10791891	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10791892	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896135	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896139	0.95[CEU][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs11227610	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11600959	0.93[ASW][hapmap];0.90[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2077432	1.00[CEU][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs2167457	0.86[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs2187041	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3741194	0.95[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs3741364	1.00[ASW][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs4576826	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4930184	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs551708	0.83[CEU][hapmap]
rs6591222	0.95[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7103627	0.86[CEU][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7119426	0.95[CEU][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs7120256	0.95[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs714766	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7930203	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7948839	0.90[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9971487	0.83[EUR][1000 genomes]

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	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv427891	chr11:66456140-66606701	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv468602	chr11:66468469-66634397	Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv555225	chr11:66468469-66634397	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv516087	chr11:66516049-66579572	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv508638	chr11:66541653-66643634	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4930390	EHBP1L1	cis	cerebellum	SCAN
rs4930390	CTSF	cis	multi-tissue	Pritchard
rs4930390	CTSF	cis	lymphoblastoid	seeQTL
rs4930390	KDM2A	cis	parietal	SCAN
rs4930390	C11orf80	cis	cerebellum	SCAN
rs4930390	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs4930390	VEGFB	cis	cerebellum	SCAN
rs4930390	B3GNT1	cis	parietal	SCAN
rs4930390	CTSF	cis	Whole Blood	GTEx
rs4930390	LRFN4	cis	multi-tissue	Pritchard

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66513400-66606800	Weak transcription	Brain Angular Gyrus	brain
2	chr11:66527000-66574200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr11:66527000-66595600	Weak transcription	HSMM	muscle
4	chr11:66527400-66571600	Weak transcription	Primary T cells from cord blood	blood
5	chr11:66530000-66571400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:66530000-66605400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:66530200-66582400	Weak transcription	HUVEC	blood vessel
8	chr11:66530600-66575200	Weak transcription	Esophagus	oesophagus
9	chr11:66530600-66600000	Weak transcription	Fetal Muscle Leg	muscle
10	chr11:66530800-66581800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:66531000-66572800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:66531200-66577800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:66531400-66578000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:66531800-66569400	Weak transcription	Brain Germinal Matrix	brain
15	chr11:66532000-66568400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:66536600-66572000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:66538200-66575800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:66539800-66571400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:66544000-66609600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:66548400-66571400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:66550400-66571400	Weak transcription	Fetal Brain Female	brain
22	chr11:66554600-66605800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr11:66554800-66568000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr11:66556200-66577600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr11:66556200-66577600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr11:66556200-66603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:66556600-66571200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:66556600-66583600	Weak transcription	Fetal Stomach	stomach
29	chr11:66556600-66586000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:66556800-66568000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:66556800-66589200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr11:66556800-66607400	Weak transcription	Fetal Lung	lung
33	chr11:66557000-66572400	Weak transcription	Thymus	Thymus
34	chr11:66557200-66567800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:66557200-66569800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:66557200-66571000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:66557200-66582400	Weak transcription	NHEK	skin
38	chr11:66557400-66568200	Weak transcription	Fetal Thymus	thymus
39	chr11:66557400-66575600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr11:66558000-66583000	Weak transcription	Hela-S3	cervix
41	chr11:66558200-66572800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr11:66558600-66560200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr11:66558600-66572800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr11:66558800-66568400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr11:66559000-66562000	Enhancers	Primary B cells from peripheral blood	blood
46	chr11:66559200-66560800	Enhancers	Primary B cells from cord blood	blood
47	chr11:66559800-66560400	Enhancers	Fetal Intestine Large	intestine
48	chr11:66560000-66560400	Enhancers	Duodenum Mucosa	Duodenum
49	chr11:66560000-66560400	Enhancers	Fetal Intestine Small	intestine
50	chr11:66560000-66560400	Enhancers	A549	lung

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