Variant report

Variant	rs61826976
Chromosome Location	chr1:227919500-227919501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:227910908-227920562	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:227915589-227919836	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr1:227914982-227921463	K562	blood:	n/a	n/a
4	POLR2A	chr1:227919226-227919757	A549	lung:	n/a	n/a
5	POLR2A	chr1:227916272-227919690	GM12891	blood:	n/a	n/a
6	POLR2A	chr1:227910941-227920625	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr1:227916673-227919956	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:227915709-227919959	GM18951	blood:	n/a	n/a
9	POLR2A	chr1:227918934-227920392	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr1:227915712-227919917	K562	blood:	n/a	n/a
11	POLR2A	chr1:227915746-227919787	GM19099	blood:	n/a	n/a
12	POLR2A	chr1:227916413-227919627	K562	blood:	n/a	n/a
13	POLR2A	chr1:227915592-227919533	MCF-7	breast:	n/a	n/a
14	POLR2A	chr1:227914179-227919823	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:227915658-227920836	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:227919270-227919527	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:227914462-227920881	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:227916824-227919789	GM12892	blood:	n/a	n/a
19	POLR2A	chr1:227914027-227920701	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:227916211-227920587	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr1:227916271-227919957	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr1:227916302-227920154	PBDE	blood:	n/a	n/a
23	POLR2A	chr1:227915700-227921841	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:227914208-227920934	K562	blood:	n/a	n/a
25	POLR2A	chr1:227915624-227920666	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:227916775-227920355	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr1:227916242-227920809	GM12892	blood:	n/a	n/a
28	POLR2A	chr1:227915660-227921896	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:227915742-227920103	GM19193	blood:	n/a	n/a
30	POLR2A	chr1:227918931-227919983	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:227919496-227919838	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:227915827-227919659	GM15510	blood:	n/a	n/a
33	POLR2A	chr1:227917695-227919551	K562	blood:	n/a	n/a
34	POLR2A	chr1:227916264-227920310	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:227915774-227919906	K562	blood:	n/a	n/a
36	POLR2A	chr1:227915672-227920956	HEK293	kidney:	n/a	n/a
37	POLR2A	chr1:227919442-227919514	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr1:227916111-227919736	GM12892	blood:	n/a	n/a
39	POLR2A	chr1:227915694-227919622	Raji	blood:	n/a	n/a
40	HEY1	chr1:227919386-227919825	K562	blood:	n/a	n/a
41	POLR2A	chr1:227916255-227921984	K562	blood:	n/a	n/a
42	POLR2A	chr1:227915629-227920059	HL-60	blood:	n/a	n/a
43	POLR2A	chr1:227919037-227919521	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:227916827-227921915	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:227916932-227919929	GM12891	blood:	n/a	n/a
46	POLR2A	chr1:227916248-227922017	SK-N-MC	brain:	n/a	n/a
47	POLR2A	chr1:227915869-227919898	NB4	blood:	n/a	n/a
48	POLR2A	chr1:227916303-227919874	K562	blood:	n/a	n/a
49	POLR2A	chr1:227917586-227919961	GM12891	blood:	n/a	n/a
50	POLR2A	chr1:227915744-227920847	GM18505	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227916734..227919516-chr1:228336405..228338652,2	MCF-7	breast:
2	chr1:227917727..227921370-chr1:227944241..227947517,4	MCF-7	breast:
3	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
4	chr1:227917861..227920741-chr1:228675887..228677861,2	MCF-7	breast:
5	chr1:227672982..227674850-chr1:227918666..227921281,2	MCF-7	breast:
6	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:

No data

Variant related genes	Relation type
SNAP47	TF binding region
ENSG00000198835	Chromatin interaction
ENSG00000230005	Chromatin interaction
ENSG00000168159	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs61824914	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs61835264	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72750259	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv3387540	chr1:227919379-227922177	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227916600-227919600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:227916800-227921600	Weak transcription	HUVEC	blood vessel
3	chr1:227917000-227919600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:227917000-227921000	Weak transcription	Hela-S3	cervix
5	chr1:227917000-227921800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:227917000-227921800	Weak transcription	Psoas Muscle	Psoas
7	chr1:227917200-227919600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:227917200-227920400	Genic enhancers	Spleen	Spleen
9	chr1:227917200-227921400	Weak transcription	Fetal Brain Male	brain
10	chr1:227917200-227921400	Weak transcription	NH-A	brain
11	chr1:227917200-227921600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:227917200-227921600	Weak transcription	Stomach Mucosa	stomach
13	chr1:227917200-227922000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:227917400-227919600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:227917400-227919600	Weak transcription	GM12878-XiMat	blood
16	chr1:227917400-227921400	Weak transcription	Primary B cells from cord blood	blood
17	chr1:227917400-227921400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:227917600-227919600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:227917600-227921400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:227917800-227920200	Strong transcription	Fetal Brain Female	brain
21	chr1:227917800-227921400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:227918000-227920000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:227918000-227921600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:227918200-227919600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:227918200-227919800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:227918200-227921200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:227918200-227921800	Genic enhancers	Fetal Muscle Leg	muscle
28	chr1:227918400-227919600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:227918400-227919800	Strong transcription	Dnd41	blood
30	chr1:227918400-227921000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:227918400-227921200	Strong transcription	Fetal Stomach	stomach
32	chr1:227918400-227921200	Strong transcription	Thymus	Thymus
33	chr1:227918400-227921800	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr1:227918400-227922000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:227918600-227919600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:227918600-227920400	Weak transcription	NHDF-Ad	bronchial
37	chr1:227918600-227920600	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:227918600-227921000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:227918600-227921000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:227918600-227921000	Strong transcription	Esophagus	oesophagus
41	chr1:227918600-227921200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:227918600-227921200	Strong transcription	HSMMtube	muscle
43	chr1:227918600-227921200	Strong transcription	NHEK	skin
44	chr1:227918600-227921400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:227918600-227921400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:227918600-227921400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:227918600-227921400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:227918600-227921400	Strong transcription	K562	blood
49	chr1:227918600-227921400	Strong transcription	NHLF	lung
50	chr1:227918600-227921600	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links