Variant report

Variant	rs11130110
Chromosome Location	chr3:47000606-47000607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47000539..47004616-chr3:47005854..47010349,8	K562	blood:
2	chr3:47000442..47004800-chr3:47015859..47022252,7	K562	blood:
3	chr3:46993850..46995776-chr3:46997950..47000879,2	MCF-7	breast:
4	chr3:46987457..46990723-chr3:46999774..47002993,3	MCF-7	breast:
5	chr3:46971047..46973675-chr3:47000415..47002568,2	MCF-7	breast:
6	chr3:46994661..46997196-chr3:47000542..47003538,2	MCF-7	breast:
7	chr3:47000243..47004408-chr3:47018008..47023852,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160796	Chromatin interaction
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10433549	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs10461018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1079276	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1108301	0.96[EUR][1000 genomes]
rs11130111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130112	1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11130115	0.93[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs1138518	0.82[JPT][hapmap]
rs11716553	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719795	0.87[JPT][hapmap]
rs11720139	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11917474	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12152493	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12491473	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12630534	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061071	0.93[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs13062681	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13066214	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13077398	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13091054	0.84[EUR][1000 genomes]
rs1463393	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17784127	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs1869869	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1869871	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2061197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2168443	0.82[JPT][hapmap]
rs2242116	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs2278963	0.89[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs2290546	0.87[JPT][hapmap]
rs2305634	0.93[ASW][hapmap];0.96[CEU][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2305635	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2305638	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2385867	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34103310	0.86[EUR][1000 genomes]
rs34344887	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4078466	0.92[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs4082155	0.93[ASW][hapmap];0.92[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs4234465	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4587	0.87[JPT][hapmap]
rs4682831	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682852	0.96[CEU][hapmap]
rs4683296	0.82[JPT][hapmap]
rs4683297	0.87[JPT][hapmap]
rs4683298	0.86[JPT][hapmap]
rs4683301	0.81[YRI][hapmap]
rs4683322	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs55843455	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56217494	0.81[EUR][1000 genomes]
rs61729713	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62246375	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62248439	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442040	0.87[JPT][hapmap]
rs66539935	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66564457	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6763236	0.85[EUR][1000 genomes]
rs6767907	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs6772670	0.95[CEU][hapmap]
rs6774733	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794193	0.84[EUR][1000 genomes]
rs6808742	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs724448	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs724449	0.82[JPT][hapmap];0.81[YRI][hapmap]
rs724450	0.82[JPT][hapmap]
rs749511	0.89[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs749512	0.82[CEU][hapmap]
rs7610636	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7617689	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7625067	0.86[EUR][1000 genomes]
rs7625070	0.86[EUR][1000 genomes]
rs7628747	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7633698	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7636252	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7637302	0.83[EUR][1000 genomes]
rs7640397	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7645278	0.87[JPT][hapmap]
rs9311403	0.92[CEU][hapmap]
rs9837343	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs9852082	0.86[JPT][hapmap]
rs9855938	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11130110	HYAL2	cis	cerebellum	SCAN
rs11130110	SCAP	cis	parietal	SCAN
rs11130110	CCDC12	cis	cerebellum	SCAN
rs11130110	CCR1	cis	cerebellum	SCAN
rs11130110	C3orf75	cis	cerebellum	SCAN
rs11130110	SCAP	cis	cerebellum	SCAN
rs11130110	PRKAR2A	cis	cerebellum	SCAN
rs11130110	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs11130110	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46985800-47004400	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr3:46988000-47003200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:46989800-47001200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:46990000-47006800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:46990200-47000800	Weak transcription	Fetal Brain Female	brain
6	chr3:46991000-47001400	Weak transcription	Osteobl	bone
7	chr3:46991200-47000800	Weak transcription	Fetal Kidney	kidney
8	chr3:46992000-47001400	Weak transcription	NHLF	lung
9	chr3:46993400-47003600	Enhancers	Fetal Heart	heart
10	chr3:46993600-47003200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr3:46994200-47001200	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr3:46994200-47001600	Enhancers	Colon Smooth Muscle	Colon
13	chr3:46994200-47002200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:46994200-47003200	Genic enhancers	Fetal Intestine Small	intestine
15	chr3:46994800-47001600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:46995000-47001600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:46995400-47002200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr3:46995400-47003200	Enhancers	Fetal Intestine Large	intestine
19	chr3:46995400-47003400	Enhancers	Primary hematopoietic stem cells	blood
20	chr3:46995600-47004200	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr3:46995800-47001400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:46995800-47001400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:46995800-47002400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:46995800-47003200	Enhancers	Primary B cells from cord blood	blood
25	chr3:46995800-47005200	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr3:46996000-47000800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:46996000-47001400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:46996000-47001400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:46996000-47001600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:46996000-47004200	Enhancers	Primary T cells from cord blood	blood
31	chr3:46996000-47004600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr3:46996000-47004800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:46996000-47007200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:46996400-47005000	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr3:46996600-47001600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:46996600-47002600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr3:46996600-47003600	Enhancers	Stomach Mucosa	stomach
38	chr3:46996800-47001400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:46998000-47000800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:46998000-47001200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:46998000-47001400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:46998400-47000800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:46998400-47002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:46998400-47003200	Genic enhancers	Dnd41	blood
45	chr3:46998600-47000800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:46998600-47000800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:46998600-47003200	Enhancers	Rectal Smooth Muscle	rectum
48	chr3:46998800-47001800	Genic enhancers	K562	blood
49	chr3:46999000-47003400	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr3:46999200-47001400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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