Variant report

Variant	rs7107498
Chromosome Location	chr11:66719481-66719482
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66717949..66720273-chr11:66722592..66724676,2	MCF-7	breast:
2	chr11:66716353..66721317-chr11:66722953..66727183,8	K562	blood:
3	chr11:66712628..66714524-chr11:66717181..66719524,2	K562	blood:
4	chr11:66698879..66700864-chr11:66717852..66719958,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173599	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1077256	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10791894	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs10791896	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11227624	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs11227625	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11227628	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11227630	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1530891	0.81[CEU][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs1901376	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4930394	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs6591226	0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs67156018	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7110302	0.86[JPT][hapmap]
rs7119682	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746018	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs746019	0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs7935749	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs7936290	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7944999	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7952017	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs966021	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[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	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv832194	chr11:66634462-66805980	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
5	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
6	esv1846713	chr11:66712229-66728044	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7107498	CDC42BPG	cis	cerebellum	SCAN
rs7107498	LRFN4	cis	multi-tissue	Pritchard
rs7107498	CCS	cis	multi-tissue	Pritchard
rs7107498	EHBP1L1	cis	cerebellum	SCAN
rs7107498	ACTN3	cis	Muscle Skeletal	GTEx
rs7107498	B3GNT1	cis	parietal	SCAN
rs7107498	SLC25A45	cis	parietal	SCAN
rs7107498	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs7107498	FGF4	cis	parietal	SCAN
rs7107498	NXF1	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66701200-66724200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr11:66701800-66719600	Weak transcription	Brain Substantia Nigra	brain
3	chr11:66702800-66723600	Weak transcription	Brain Angular Gyrus	brain
4	chr11:66708000-66724200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr11:66708200-66724200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:66708600-66724200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:66708600-66724200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr11:66709200-66719600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:66709400-66724400	Weak transcription	Brain Germinal Matrix	brain
10	chr11:66711200-66719600	Weak transcription	Fetal Stomach	stomach
11	chr11:66713600-66724200	Weak transcription	Spleen	Spleen
12	chr11:66714400-66724400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:66716200-66719600	Weak transcription	Adipose Nuclei	Adipose
14	chr11:66716200-66725200	Weak transcription	Aorta	Aorta
15	chr11:66716400-66724200	Weak transcription	Dnd41	blood
16	chr11:66716400-66725200	Weak transcription	Lung	lung
17	chr11:66716800-66719600	Weak transcription	Fetal Lung	lung
18	chr11:66717200-66719800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr11:66717200-66720800	Enhancers	Placenta	Placenta
20	chr11:66717200-66724200	Weak transcription	Fetal Intestine Large	intestine
21	chr11:66717600-66720000	Enhancers	HepG2	liver
22	chr11:66717600-66720800	Enhancers	Fetal Muscle Leg	muscle
23	chr11:66717600-66722000	Strong transcription	Brain Cingulate Gyrus	brain
24	chr11:66717800-66721400	Strong transcription	Primary T cells from cord blood	blood
25	chr11:66717800-66724000	Weak transcription	Fetal Kidney	kidney
26	chr11:66717800-66724200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:66717800-66725000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:66718000-66719600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:66718000-66719800	Strong transcription	Liver	Liver
30	chr11:66718000-66724200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr11:66718000-66724400	Weak transcription	Esophagus	oesophagus
32	chr11:66718000-66724600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:66718200-66719600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr11:66718200-66719600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:66718200-66719600	Weak transcription	HUVEC	blood vessel
36	chr11:66718200-66719600	Weak transcription	NHLF	lung
37	chr11:66718200-66720000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr11:66718200-66721400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:66718200-66721600	Strong transcription	Fetal Brain Female	brain
40	chr11:66718200-66723000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:66718200-66724200	Weak transcription	NH-A	brain
42	chr11:66718200-66724600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr11:66718200-66724800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr11:66718400-66719600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:66718400-66720000	Genic enhancers	A549	lung
46	chr11:66718400-66723600	Weak transcription	Osteobl	bone
47	chr11:66718400-66724400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:66718600-66719600	Weak transcription	Brain Anterior Caudate	brain
49	chr11:66718600-66720000	Strong transcription	NHEK	skin
50	chr11:66718600-66723600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links