Variant report

Variant	rs2061197
Chromosome Location	chr3:47001350-47001351
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

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	chr3:47000992..47003826-chr3:47019439..47023758,5	MCF-7	breast:
4	chr3:46979541..46981499-chr3:47001280..47002981,2	K562	blood:
5	chr3:46973841..46975600-chr3:47001098..47002983,2	MCF-7	breast:
6	chr3:46987457..46990723-chr3:46999774..47002993,3	MCF-7	breast:
7	chr3:46971047..46973675-chr3:47000415..47002568,2	MCF-7	breast:
8	chr3:46994661..46997196-chr3:47000542..47003538,2	MCF-7	breast:
9	chr3:47000243..47004408-chr3:47018008..47023852,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160796	Chromatin interaction
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10433549	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs10461018	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1079276	0.96[CEU][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1108301	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11130110	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]
rs11130111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130112	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11130115	0.96[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap]
rs1138518	0.82[JPT][hapmap];0.82[LWK][hapmap]
rs11716553	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11719795	0.87[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap]
rs11720139	0.88[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs11917474	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12152493	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12491473	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12630534	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061071	0.96[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs13062681	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13066214	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13077398	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13091054	0.83[EUR][1000 genomes]
rs1463393	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17784127	0.85[CEU][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs1869869	0.96[EUR][1000 genomes]
rs1869871	0.87[EUR][1000 genomes]
rs2168443	0.82[JPT][hapmap];0.82[LWK][hapmap]
rs2242116	0.82[JPT][hapmap]
rs2278963	0.91[ASW][hapmap];0.89[CEU][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs2290546	0.87[JPT][hapmap]
rs2305634	0.96[CEU][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2305635	0.88[CEU][hapmap];0.90[YRI][hapmap];0.85[EUR][1000 genomes]
rs2305638	0.88[CEU][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2385867	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34103310	0.85[EUR][1000 genomes]
rs34344887	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4078466	0.92[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4082155	0.92[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4234465	1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4587	0.87[JPT][hapmap]
rs4682831	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682844	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682852	0.96[CEU][hapmap]
rs4683296	0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4683297	0.91[ASW][hapmap];0.87[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4683298	0.86[JPT][hapmap]
rs4683322	0.91[ASW][hapmap];0.89[CEU][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap]
rs55724164	0.80[EUR][1000 genomes]
rs55843455	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56217494	0.81[EUR][1000 genomes]
rs61729713	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62246375	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62248439	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442040	0.87[JPT][hapmap];0.83[MEX][hapmap]
rs66539935	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66564457	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6763236	0.85[EUR][1000 genomes]
rs6767218	0.80[EUR][1000 genomes]
rs6767907	0.83[ASW][hapmap];0.89[CEU][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap]
rs6772670	0.95[CEU][hapmap]
rs6774733	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6794193	0.84[EUR][1000 genomes]
rs6808742	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs724448	0.81[JPT][hapmap]
rs724449	0.82[JPT][hapmap]
rs724450	0.82[JPT][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap]
rs7433300	0.91[ASW][hapmap];0.91[YRI][hapmap]
rs749511	0.89[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs749512	0.91[ASW][hapmap];0.82[CEU][hapmap];1.00[YRI][hapmap]
rs7610636	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7617689	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7623898	0.82[AFR][1000 genomes]
rs7625067	0.85[EUR][1000 genomes]
rs7625070	0.85[EUR][1000 genomes]
rs7628747	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];0.98[ASN][1000 genomes]
rs7633698	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7636252	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7637302	0.82[EUR][1000 genomes]
rs7640397	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7645278	0.91[ASW][hapmap];0.87[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9311403	0.92[CEU][hapmap];0.91[YRI][hapmap]
rs9837343	0.83[ASW][hapmap];0.89[CEU][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap]
rs9852082	0.86[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
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
rs2061197	CCDC12	cis	cerebellum	SCAN
rs2061197	PRKAR2A	cis	cerebellum	SCAN
rs2061197	SCAP	cis	parietal	SCAN
rs2061197	SCAP	cis	cerebellum	SCAN
rs2061197	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs2061197	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs2061197	C3orf75	cis	cerebellum	SCAN
rs2061197	HYAL2	cis	cerebellum	SCAN
rs2061197	CCR1	cis	cerebellum	SCAN

Chromatin state (count:125 , 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	chr3:46990000-47006800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:46991000-47001400	Weak transcription	Osteobl	bone
5	chr3:46992000-47001400	Weak transcription	NHLF	lung
6	chr3:46993400-47003600	Enhancers	Fetal Heart	heart
7	chr3:46993600-47003200	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr3:46994200-47001600	Enhancers	Colon Smooth Muscle	Colon
9	chr3:46994200-47002200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:46994200-47003200	Genic enhancers	Fetal Intestine Small	intestine
11	chr3:46994800-47001600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:46995000-47001600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:46995400-47002200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr3:46995400-47003200	Enhancers	Fetal Intestine Large	intestine
15	chr3:46995400-47003400	Enhancers	Primary hematopoietic stem cells	blood
16	chr3:46995600-47004200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr3:46995800-47001400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:46995800-47001400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:46995800-47002400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:46995800-47003200	Enhancers	Primary B cells from cord blood	blood
21	chr3:46995800-47005200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr3:46996000-47001400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:46996000-47001400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:46996000-47001600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:46996000-47004200	Enhancers	Primary T cells from cord blood	blood
26	chr3:46996000-47004600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr3:46996000-47004800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:46996000-47007200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:46996400-47005000	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr3:46996600-47001600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:46996600-47002600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr3:46996600-47003600	Enhancers	Stomach Mucosa	stomach
33	chr3:46996800-47001400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:46998000-47001400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:46998400-47002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:46998400-47003200	Genic enhancers	Dnd41	blood
37	chr3:46998600-47003200	Enhancers	Rectal Smooth Muscle	rectum
38	chr3:46998800-47001800	Genic enhancers	K562	blood
39	chr3:46999000-47003400	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr3:46999200-47001400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:46999200-47002400	Weak transcription	Aorta	Aorta
42	chr3:46999200-47003200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:46999200-47003600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:46999200-47004400	Enhancers	Liver	Liver
45	chr3:46999600-47002000	Weak transcription	A549	lung
46	chr3:46999600-47003600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:46999800-47002200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:46999800-47003200	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr3:46999800-47003200	Genic enhancers	Fetal Thymus	thymus
50	chr3:46999800-47003200	Enhancers	Ovary	ovary

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