Variant report

Variant	rs6719
Chromosome Location	chr1:154179679-154179680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154177678-154180202	K562	blood:	n/a	n/a
2	POLR2A	chr1:154177691-154180265	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:154179311-154179755	K562	blood:	n/a	n/a
4	POLR2A	chr1:154179639-154182756	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr1:154179157-154179855	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr1:154177962-154183356	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:154179671-154179742	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:154179265-154179746	HepG2	liver:	n/a	n/a
9	SP1	chr1:154179137-154180181	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154152910..154155985-chr1:154176488..154179732,3	K562	blood:
2	chr1:154177747..154182716-chr1:154190412..154196946,9	K562	blood:
3	chr1:154164207..154166951-chr1:154178142..154180976,3	K562	blood:
4	chr1:154179575..154184047-chr1:154184381..154189147,7	K562	blood:
5	chr1:154164207..154166650-chr1:154177801..154180976,3	K562	blood:
6	chr1:154179244..154180954-chr1:154181456..154183378,2	K562	blood:
7	chr1:154153345..154155827-chr1:154177952..154179974,2	K562	blood:
8	chr1:154178712..154180249-chr1:154186169..154187712,2	MCF-7	breast:

No data

Variant related genes	Relation type
C1orf189	TF binding region
ENSG00000143549	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000215938	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10158820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1044013	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10797047	0.91[ASN][1000 genomes]
rs10797061	0.81[GIH][hapmap]
rs11265238	0.91[JPT][hapmap]
rs11265251	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265299	0.82[EUR][1000 genomes]
rs11265425	0.95[JPT][hapmap]
rs11802893	0.86[JPT][hapmap]
rs1194580	0.81[GIH][hapmap]
rs1194593	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1194596	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1194603	0.81[GIH][hapmap]
rs1194604	0.81[GIH][hapmap]
rs12023901	0.85[ASN][1000 genomes]
rs12025237	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12026177	0.91[JPT][hapmap]
rs12026615	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12027999	0.86[ASN][1000 genomes]
rs12028554	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12028949	0.91[JPT][hapmap]
rs12029331	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12062977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12408458	0.82[EUR][1000 genomes]
rs12733060	0.86[ASN][1000 genomes]
rs12738393	0.86[ASN][1000 genomes]
rs16835846	0.87[JPT][hapmap]
rs16835852	0.87[JPT][hapmap]
rs1760802	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs1760803	0.81[ASN][1000 genomes]
rs1986709	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2220390	0.81[GIH][hapmap]
rs2274993	0.83[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2282227	0.82[ASN][1000 genomes]
rs2340473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2879788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762339	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3762340	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3790613	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3790614	0.86[ASN][1000 genomes]
rs3811453	0.83[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3811455	0.91[JPT][hapmap]
rs3828077	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3935419	0.91[JPT][hapmap]
rs4240871	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4620534	0.91[JPT][hapmap]
rs6427509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657214	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6667222	0.84[YRI][hapmap]
rs6673752	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7517578	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7524346	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7551128	0.82[EUR][1000 genomes]
rs9803857	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9803862	0.81[GIH][hapmap]
rs9804045	0.81[GIH][hapmap]
rs9943093	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' 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	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	nsv946405	chr1:154179146-154180987	Genic enhancers Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6719	CRTC2	cis	cerebellum	SCAN
rs6719	LCE1C	cis	cerebellum	SCAN
rs6719	HAX1	cis	lymphoblastoid	seeQTL
rs6719	C1orf43	cis	parietal	SCAN
rs6719	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL
rs6719	SPRR2D	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154159000-154184400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:154172000-154180600	Weak transcription	Small Intestine	intestine
3	chr1:154172000-154184600	Weak transcription	Fetal Brain Male	brain
4	chr1:154172200-154184200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:154172200-154190000	Weak transcription	Fetal Heart	heart
6	chr1:154172400-154184600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:154176400-154179800	Weak transcription	Right Ventricle	heart
8	chr1:154177000-154191000	Strong transcription	Fetal Stomach	stomach
9	chr1:154177000-154192000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:154177200-154180200	Strong transcription	Colon Smooth Muscle	Colon
11	chr1:154177200-154187200	Strong transcription	Brain Hippocampus Middle	brain
12	chr1:154177200-154187400	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:154177200-154187600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:154177200-154190200	Strong transcription	Primary T cells from cord blood	blood
15	chr1:154177400-154190400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:154177600-154181000	Strong transcription	Brain Cingulate Gyrus	brain
17	chr1:154177600-154184600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:154177600-154184800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:154177600-154187000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:154177600-154187000	Strong transcription	Adipose Nuclei	Adipose
21	chr1:154177600-154187000	Strong transcription	Fetal Brain Female	brain
22	chr1:154177600-154187200	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:154177600-154187400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:154177600-154187400	Strong transcription	Fetal Thymus	thymus
25	chr1:154177600-154191400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:154177800-154180200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:154177800-154185600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:154177800-154185800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:154177800-154186000	Strong transcription	A549	lung
30	chr1:154177800-154186200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:154177800-154186800	Strong transcription	Liver	Liver
32	chr1:154177800-154187200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:154177800-154187200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr1:154177800-154187200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:154177800-154187200	Strong transcription	Brain Substantia Nigra	brain
36	chr1:154177800-154187200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:154177800-154187200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr1:154177800-154187400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:154177800-154187400	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:154177800-154187400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:154177800-154187400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:154177800-154187400	Strong transcription	Fetal Intestine Large	intestine
43	chr1:154177800-154187600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:154177800-154188000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr1:154177800-154190400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:154177800-154190600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:154177800-154190600	Strong transcription	Fetal Intestine Small	intestine
48	chr1:154177800-154191000	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:154177800-154191400	Strong transcription	Placenta	Placenta
50	chr1:154178000-154180200	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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