Variant report

Variant	rs4771704
Chromosome Location	chr13:111296170-111296171
allele	C/T
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	chr13:111266678..111269187-chr13:111295319..111298212,3	MCF-7	breast:
2	chr13:111266944..111268705-chr13:111296076..111298471,2	K562	blood:
3	chr13:111295643..111300120-chr13:111365518..111369026,8	MCF-7	breast:
4	chr13:111292549..111296522-chr13:111365011..111368169,4	MCF-7	breast:
5	chr13:111294769..111296453-chr13:111366037..111368687,3	K562	blood:
6	chr13:111295887..111296636-chr19:10443828..10444619,2	NB4	blood:
7	chr13:111294769..111302902-chr13:111363368..111369699,14	K562	blood:
8	chr13:111266655..111268705-chr13:111294879..111298471,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134905	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000213995	Chromatin interaction
ENSG00000161847	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11069856	0.82[JPT][hapmap]
rs12429651	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12429905	0.80[JPT][hapmap]
rs12430171	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12584848	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1853860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1853861	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs2296655	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2296656	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2296658	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs2296659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs28384426	0.80[JPT][hapmap]
rs28683030	0.89[ASN][1000 genomes]
rs2986104	0.80[ASN][1000 genomes]
rs365103	0.87[ASN][1000 genomes]
rs3742193	0.90[JPT][hapmap]
rs3742194	0.90[JPT][hapmap]
rs3742196	0.90[JPT][hapmap]
rs3742201	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs376834	0.85[ASN][1000 genomes]
rs388049	0.81[ASN][1000 genomes]
rs4238278	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs4268629	0.84[ASN][1000 genomes]
rs4628819	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs4771702	0.91[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4771703	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4771706	0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4773232	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59261018	0.94[ASN][1000 genomes]
rs66605126	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs718341	1.00[CHB][hapmap]
rs72661663	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72661672	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72661683	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7323602	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs7328567	0.87[ASN][1000 genomes]
rs7328764	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs7335010	0.85[ASN][1000 genomes]
rs7335538	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs7336134	0.83[ASN][1000 genomes]
rs7336283	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs7399501	0.83[ASN][1000 genomes]
rs7984290	0.87[ASN][1000 genomes]
rs7985128	0.87[ASN][1000 genomes]
rs7985899	0.83[ASN][1000 genomes]
rs7993933	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8000867	0.87[ASN][1000 genomes]
rs9521888	0.80[ASN][1000 genomes]
rs9521893	0.85[ASN][1000 genomes]
rs9583520	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9583523	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9583524	0.82[ASN][1000 genomes]
rs9588214	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs9588235	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
2	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
3	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS 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	25 gene(s)	inside rSNPs	diseases
5	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS 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
6	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS 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
8	nsv901012	chr13:111220842-111340342	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
10	nsv563124	chr13:111261267-111300943	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
12	nsv456120	chr13:111280002-111309617	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	n/a
13	nsv563125	chr13:111280002-111309617	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	n/a
14	nsv1042232	chr13:111282123-111348475	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
15	nsv901013	chr13:111291192-111340342	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4771704	AL139385.1	cis	Muscle Skeletal	GTEx
rs4771704	GRTP1	cis	cerebellum	SCAN
rs4771704	CARKD	cis	Muscle Skeletal	GTEx
rs4771704	CARKD	cis	parietal	SCAN
rs4771704	TUBGCP3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111270800-111296800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:111280800-111328600	Weak transcription	Psoas Muscle	Psoas
3	chr13:111282000-111309600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr13:111282800-111310000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr13:111285800-111296800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr13:111286000-111297000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr13:111286000-111297000	Strong transcription	Fetal Intestine Large	intestine
8	chr13:111286000-111297000	Strong transcription	Fetal Intestine Small	intestine
9	chr13:111286000-111297200	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr13:111286000-111297400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr13:111286000-111298200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr13:111286200-111296200	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr13:111286200-111296800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:111286200-111296800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr13:111286200-111296800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr13:111286200-111296800	Strong transcription	Gastric	stomach
17	chr13:111286200-111297000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:111286200-111297000	Strong transcription	Duodenum Mucosa	Duodenum
19	chr13:111286200-111297000	Strong transcription	Fetal Thymus	thymus
20	chr13:111286200-111297200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr13:111286200-111297400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr13:111286200-111299600	Strong transcription	Placenta	Placenta
23	chr13:111286200-111308400	Strong transcription	Dnd41	blood
24	chr13:111286400-111296800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr13:111286400-111296800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr13:111286400-111296800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr13:111286400-111297000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr13:111286400-111297000	Strong transcription	Primary T cells from cord blood	blood
29	chr13:111286400-111297000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr13:111286400-111297000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr13:111286400-111297200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr13:111286400-111297400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr13:111286400-111299800	Strong transcription	HepG2	liver
34	chr13:111286400-111300400	Strong transcription	Thymus	Thymus
35	chr13:111286400-111308200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:111286600-111296400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr13:111286600-111296600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr13:111286600-111296600	Strong transcription	Brain Germinal Matrix	brain
39	chr13:111286600-111296800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr13:111286600-111296800	Strong transcription	Brain Hippocampus Middle	brain
41	chr13:111286600-111297000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr13:111286600-111297000	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr13:111286600-111297000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr13:111286600-111297200	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr13:111286800-111296600	Strong transcription	Primary B cells from cord blood	blood
46	chr13:111286800-111296800	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr13:111286800-111296800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr13:111286800-111296800	Strong transcription	Brain Substantia Nigra	brain
49	chr13:111286800-111296800	Strong transcription	Fetal Lung	lung
50	chr13:111286800-111297000	Strong transcription	Colonic Mucosa	Colon

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