Variant report

Variant	rs1701706
Chromosome Location	chr12:56402204-56402205
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56401586-56402225	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr12:56400540-56402452	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr12:56400758-56402521	H1-neurons	neurons:	n/a	chr12:56401778-56401791
4	TAF1	chr12:56400685-56402279	ECC-1	luminal epithelium:	n/a	n/a
5	TAF1	chr12:56401580-56402259	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:56400804-56402240	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:56401562-56402235	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56399175..56403137-chr12:56403716..56405667,4	MCF-7	breast:
2	chr12:56398217..56408038-chr12:56433794..56439966,15	K562	blood:
3	chr12:56364817..56368355-chr12:56399269..56402650,4	K562	blood:
4	chr12:56400102..56402586-chr12:56415416..56418384,2	MCF-7	breast:
5	chr12:56224367..56226323-chr12:56401356..56403743,2	MCF-7	breast:
6	chr12:56360672..56362289-chr12:56400535..56402399,2	MCF-7	breast:
7	chr12:56122770..56125786-chr12:56400050..56403264,3	K562	blood:
8	chr12:56400915..56403340-chr12:56510572..56513192,4	MCF-7	breast:
9	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
10	chr12:56389364..56393818-chr12:56396293..56409099,19	MCF-7	breast:
11	chr12:56399898..56405642-chr12:56433175..56438589,7	K562	blood:
12	chr12:56211633..56216017-chr12:56399885..56403410,4	MCF-7	breast:
13	chr12:56399605..56402732-chr12:56433705..56437280,6	MCF-7	breast:
14	chr12:56390809..56392348-chr12:56401235..56403925,2	K562	blood:
15	chr12:56400079..56406275-chr12:56406695..56413732,8	MCF-7	breast:
16	chr12:56399990..56402705-chr12:56510349..56512541,3	K562	blood:
17	chr12:56401139..56403498-chr12:56475848..56478502,3	K562	blood:
18	chr12:56222087..56223926-chr12:56400815..56402785,2	MCF-7	breast:
19	chr12:56318939..56322802-chr12:56399424..56402892,5	MCF-7	breast:
20	chr12:56323623..56326295-chr12:56400061..56402642,2	MCF-7	breast:
21	chr12:56386715..56395273-chr12:56398367..56404356,15	MCF-7	breast:

No data

Variant related genes	Relation type
IKZF4	TF binding region
ENSG00000182796	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000065361	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11171713	0.88[CEU][hapmap]
rs11550558	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs12099979	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs1274298	1.00[CHD][hapmap]
rs12810011	0.91[EUR][1000 genomes]
rs12810816	1.00[CHD][hapmap]
rs12815302	0.86[EUR][1000 genomes]
rs12815387	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12815488	0.91[EUR][1000 genomes]
rs12818756	0.91[EUR][1000 genomes]
rs12831468	0.91[EUR][1000 genomes]
rs12831884	1.00[CEU][hapmap]
rs1290898	1.00[CHD][hapmap]
rs1614219	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1689511	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1702876	0.83[AFR][1000 genomes]
rs17118206	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs17118208	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs17118262	0.91[EUR][1000 genomes]
rs17118313	1.00[CHD][hapmap]
rs2131569	0.98[EUR][1000 genomes]
rs2456972	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2658479	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34228181	0.91[EUR][1000 genomes]
rs34303864	0.91[EUR][1000 genomes]
rs34406511	0.91[EUR][1000 genomes]
rs34485293	0.89[EUR][1000 genomes]
rs34507011	0.96[EUR][1000 genomes]
rs34602183	0.87[EUR][1000 genomes]
rs34650555	0.91[EUR][1000 genomes]
rs34921584	0.91[EUR][1000 genomes]
rs35436573	1.00[CHD][hapmap]
rs35485002	0.94[EUR][1000 genomes]
rs35961650	0.93[EUR][1000 genomes]
rs4759022	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4759239	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71459334	0.91[EUR][1000 genomes]
rs71459336	0.89[EUR][1000 genomes]
rs71459339	0.91[EUR][1000 genomes]
rs7298818	0.92[EUR][1000 genomes]
rs7300772	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs772919	0.88[EUR][1000 genomes]
rs772922	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs772923	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs773115	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs773120	1.00[CHD][hapmap]
rs773121	1.00[CHD][hapmap]
rs773122	1.00[CHD][hapmap]
rs773643	1.00[CHD][hapmap]
rs773649	1.00[CHD][hapmap]
rs7963590	0.87[EUR][1000 genomes]
rs7977537	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3444965	chr12:56400510-56402733	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1701706	RDH5	cis	lymphoblastoid	seeQTL
rs1701706	LOC441377	trans	multi-tissue	Pritchard
rs1701706	LOC644934	trans	multi-tissue	Pritchard
rs1701706	RPS26	cis	lymphoblastoid	seeQTL
rs1701706	RPS26P10	trans	multi-tissue	Pritchard
rs1701706	LOC441502	trans	multi-tissue	Pritchard
rs1701706	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs1701706	RPS26	cis	multi-tissue	Pritchard
rs1701706	CCDC4	trans	multi-tissue	Pritchard

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56400600-56402400	Active TSS	H1 Cell Line	embryonic stem cell
2	chr12:56400600-56402400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr12:56400600-56402400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:56400600-56402400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr12:56400600-56402400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr12:56400600-56402400	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr12:56400600-56402400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:56400600-56402400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:56400600-56402400	Active TSS	Colon Smooth Muscle	Colon
10	chr12:56400600-56402400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr12:56400800-56402400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr12:56400800-56402400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:56400800-56402400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:56400800-56402400	Active TSS	Ovary	ovary
15	chr12:56401000-56402400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:56401600-56402400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:56401600-56402400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:56401600-56402400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:56401600-56402400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:56401800-56402400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:56401800-56402400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:56401800-56402400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr12:56401800-56402400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:56401800-56402400	Flanking Active TSS	Fetal Brain Female	brain
25	chr12:56401800-56402400	Flanking Active TSS	Fetal Intestine Large	intestine
26	chr12:56401800-56402400	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr12:56401800-56402400	Flanking Active TSS	Osteobl	bone
28	chr12:56402000-56402400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr12:56402000-56402400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:56402000-56402400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr12:56402000-56402400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr12:56402000-56402400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:56402000-56402400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:56402000-56402400	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:56402000-56402400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr12:56402000-56402400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:56402000-56402400	Flanking Active TSS	Fetal Kidney	kidney
38	chr12:56402000-56402400	Flanking Active TSS	Fetal Lung	lung
39	chr12:56402000-56418600	Weak transcription	Gastric	stomach
40	chr12:56402200-56402400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:56402200-56402400	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr12:56402200-56402400	Enhancers	Primary T cells from cord blood	blood
43	chr12:56402200-56402400	Enhancers	Primary T cells fromperipheralblood	blood
44	chr12:56402200-56402400	Enhancers	Primary hematopoietic stem cells	blood
45	chr12:56402200-56402400	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr12:56402200-56402400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr12:56402200-56402400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr12:56402200-56402400	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr12:56402200-56402400	Active TSS	Muscle Satellite Cultured Cells	--
50	chr12:56402200-56402400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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