Variant report

Variant	rs16835852
Chromosome Location	chr1:154127820-154127821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:1)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154126848-154127883	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:154127428-154128204	K562	blood:	n/a	n/a
3	POLR2A	chr1:154126201-154128392	U87	brain:	n/a	n/a
4	POLR2A	chr1:154126673-154128315	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr1:154127801-154128075	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:154127805-154128152	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr1:154126850-154128357	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:154126077-154128299	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr1:154127776-154128078	K562	blood:	n/a	n/a
10	POLR2A	chr1:154126931-154128239	GM12891	blood:	n/a	n/a
11	POLR2A	chr1:154126957-154128168	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:154126854-154128608	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr1:154127370-154128385	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:154126751-154128167	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:154126532-154128374	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr1:154127360-154128463	GM12892	blood:	n/a	n/a
17	GATA1	chr1:154127472-154128477	PBDE	blood:	n/a	n/a
18	POLR2A	chr1:154126745-154128076	GM12891	blood:	n/a	n/a
19	CREB1	chr1:154127273-154127854	H1-hESC	embryonic stem cell:	n/a	chr1:154127589-154127602
20	POLR2A	chr1:154126091-154128677	PFSK-1	brain:	n/a	n/a
21	PML	chr1:154126861-154128129	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:154127344-154128436	K562	blood:	n/a	n/a
23	POLR2A	chr1:154127772-154128151	HUVEC	blood vessel:	n/a	n/a
24	CCNT2	chr1:154127508-154128008	K562	blood:	n/a	n/a
25	POLR2A	chr1:154127729-154128193	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr1:154126919-154128203	GM12891	blood:	n/a	n/a
27	POLR2A	chr1:154126883-154128299	HL-60	blood:	n/a	n/a
28	POLR2A	chr1:154126172-154128709	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr1:154126858-154128169	HL-60	blood:	n/a	n/a
30	CREB1	chr1:154127332-154127837	H1-hESC	embryonic stem cell:	n/a	chr1:154127589-154127602
31	POLR2A	chr1:154126447-154128372	A549	lung:	n/a	n/a
32	POLR2A	chr1:154126938-154128434	GM12892	blood:	n/a	n/a
33	POLR2A	chr1:154127212-154128352	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr1:154126411-154128102	GM12891	blood:	n/a	n/a
35	POLR2A	chr1:154126864-154128753	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:154126284-154128518	K562	blood:	n/a	n/a
37	POLR2A	chr1:154126845-154129319	GM12892	blood:	n/a	n/a
38	MTA3	chr1:154126661-154128099	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:154126260-154127848	U87	brain:	n/a	n/a
40	ZMIZ1	chr1:154127638-154127836	K562	blood:	n/a	n/a
41	E2F6	chr1:154126932-154127866	H1-hESC	embryonic stem cell:	n/a	chr1:154127590-154127599 chr1:154127592-154127601
42	POLR2A	chr1:154126950-154128184	Hela-S3	cervix:	n/a	n/a
43	TBL1XR1	chr1:154127525-154127828	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153962389..153965646-chr1:154127758..154130394,3	K562	blood:
2	chr1:154122896..154125457-chr1:154127729..154131254,3	MCF-7	breast:
3	chr1:154127794..154129352-chr1:154153718..154155371,2	K562	blood:

No data

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

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	TPM3	hsa-miR-145-5p	chr1:154127807-154127829

Variant related genes	Relation type
NUP210L	TF binding region
ENSG00000177954	Chromatin interaction
TPM3	miRNA target site

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10158820	0.84[JPT][hapmap]
rs1044013	0.87[JPT][hapmap]
rs11265238	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11265251	0.87[JPT][hapmap]
rs11265425	0.91[JPT][hapmap]
rs11802893	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1194594	0.83[YRI][hapmap]
rs1194596	0.87[JPT][hapmap]
rs1194597	0.91[YRI][hapmap]
rs1194601	1.00[YRI][hapmap]
rs1194605	0.87[YRI][hapmap]
rs12025237	0.87[JPT][hapmap]
rs12026177	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12026615	0.91[JPT][hapmap]
rs12028949	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12038362	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12043131	0.90[CEU][hapmap]
rs1205590	0.87[YRI][hapmap]
rs12062977	0.84[JPT][hapmap]
rs16835846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1760802	0.83[JPT][hapmap]
rs2274993	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs2340473	0.82[JPT][hapmap]
rs2500222	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2633434	0.85[YRI][hapmap]
rs2790689	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs28372838	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2879788	0.83[JPT][hapmap]
rs3002660	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34128679	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34335016	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35761479	0.84[EUR][1000 genomes]
rs3762340	0.82[CEU][hapmap];0.87[JPT][hapmap]
rs3790613	0.87[JPT][hapmap]
rs3811453	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs3811455	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3828077	0.87[JPT][hapmap]
rs3935419	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4433384	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4459102	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs4620534	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60282844	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427509	0.83[JPT][hapmap]
rs6673752	0.87[JPT][hapmap]
rs6676022	0.82[EUR][1000 genomes]
rs6719	0.87[JPT][hapmap]
rs9803857	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv520398	chr1:154068196-154141908	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv872451	chr1:154101519-154139757	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154112200-154138400	Weak transcription	Psoas Muscle	Psoas
2	chr1:154124000-154128000	Weak transcription	NHDF-Ad	bronchial
3	chr1:154124400-154129800	Weak transcription	Left Ventricle	heart
4	chr1:154125000-154130400	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:154125200-154131000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr1:154125400-154128000	Weak transcription	Stomach Mucosa	stomach
7	chr1:154125600-154128000	Weak transcription	NHEK	skin
8	chr1:154125600-154129800	Weak transcription	Brain Angular Gyrus	brain
9	chr1:154125600-154129800	Weak transcription	Gastric	stomach
10	chr1:154125600-154130000	Weak transcription	Brain Germinal Matrix	brain
11	chr1:154125800-154129600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:154126000-154128000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:154126200-154128200	Genic enhancers	Primary T cells from cord blood	blood
14	chr1:154126200-154128600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:154126200-154128800	Genic enhancers	Primary hematopoietic stem cells	blood
16	chr1:154126200-154128800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:154126200-154129400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:154126200-154129400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr1:154126200-154129600	Weak transcription	HSMMtube	muscle
20	chr1:154126200-154130400	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr1:154126400-154128600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:154126400-154128600	Strong transcription	Thymus	Thymus
23	chr1:154126400-154129600	Genic enhancers	K562	blood
24	chr1:154126400-154129600	Genic enhancers	NHLF	lung
25	chr1:154126400-154129800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr1:154126400-154129800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:154126400-154130400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:154126400-154133000	Weak transcription	Ovary	ovary
29	chr1:154126400-154146000	Strong transcription	HMEC	breast
30	chr1:154126600-154128200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:154126600-154129600	Weak transcription	HepG2	liver
32	chr1:154126600-154130200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:154126800-154128600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:154126800-154129800	Strong transcription	GM12878-XiMat	blood
35	chr1:154126800-154130000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
36	chr1:154126800-154130200	Weak transcription	Fetal Brain Male	brain
37	chr1:154126800-154131600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:154127000-154128000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:154127000-154128200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:154127000-154128200	Genic enhancers	Fetal Stomach	stomach
41	chr1:154127000-154128400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:154127000-154128400	Enhancers	Colon Smooth Muscle	Colon
43	chr1:154127000-154128400	Enhancers	Fetal Lung	lung
44	chr1:154127000-154128400	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr1:154127000-154129400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
46	chr1:154127000-154129600	Strong transcription	Dnd41	blood
47	chr1:154127000-154130200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:154127000-154130200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:154127000-154130200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
50	chr1:154127000-154130200	Strong transcription	Fetal Intestine Small	intestine

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