Variant report

Variant	rs7641976
Chromosome Location	chr3:49724330-49724331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr3:49723750-49724734	H1-hESC	embryonic stem cell:	n/a	n/a
2	TAF1	chr3:49723221-49724844	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:49723711-49724551	PANC-1	pancreas:	n/a	n/a
4	ZBTB33	chr3:49723901-49724576	K562	blood:	n/a	n/a
5	POLR2A	chr3:49723697-49724625	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:49721456-49727648	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:49723734-49725129	GM12878	blood:	n/a	n/a
8	SIN3A	chr3:49723769-49724762	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:49724225-49724470	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:49717503-49727239	HepG2	liver:	n/a	n/a
11	TCF3	chr3:49724018-49724651	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:49720128-49724935	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:49722602-49725401	H1-hESC	embryonic stem cell:	n/a	n/a
14	ZBTB33	chr3:49723668-49724629	K562	blood:	n/a	n/a
15	POLR2A	chr3:49716580-49724829	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:49723657-49724615	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr3:49724225-49724522	A549	lung:	n/a	n/a
18	SP1	chr3:49724215-49724529	GM12878	blood:	n/a	n/a
19	EGR1	chr3:49724143-49724571	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr3:49723963-49724472	U87	brain:	n/a	n/a
21	POU2F2	chr3:49723701-49724861	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:49723134-49724607	A549	lung:	n/a	n/a
23	ZBTB33	chr3:49724302-49724569	GM12878	blood:	n/a	n/a
24	TAF1	chr3:49723406-49724769	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr3:49723739-49724949	H1-hESC	embryonic stem cell:	n/a	n/a
26	PAX5	chr3:49723891-49724704	GM12878	blood:	n/a	n/a
27	EBF1	chr3:49724207-49724617	GM12878	blood:	n/a	n/a
28	HEY1	chr3:49718256-49727412	HepG2	liver:	n/a	n/a
29	POLR2A	chr3:49724156-49724780	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr3:49724026-49724639	PBDE	blood:	n/a	n/a
31	POLR2A	chr3:49723796-49724749	SK-N-MC	brain:	n/a	n/a
32	POLR2A	chr3:49722625-49725083	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:49721241-49724664	GM12892	blood:	n/a	n/a
34	POLR2A	chr3:49724137-49724677	ECC-1	luminal epithelium:	n/a	n/a
35	PAX5	chr3:49724291-49724478	GM12878	blood:	n/a	n/a
36	TEAD4	chr3:49723603-49724557	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr3:49721694-49724714	GM12878	blood:	n/a	n/a
38	FOSL2	chr3:49723695-49727217	HepG2	liver:	n/a	n/a
39	POLR2A	chr3:49723741-49724547	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr3:49724305-49724532	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:49724291-49724341	AG04449	skin:	fetal
2	chr3:49724291-49724341	NH-A	brain:	n/a
3	chr3:49724291-49724341	HUVEC	blood vessel:	n/a
4	chr3:49724291-49724341	ECC-1	luminal epithelium:	n/a
5	chr3:49724291-49724341	HepG2	liver:	n/a
6	chr3:49724291-49724341	Caco-2	colon:	n/a
7	chr3:49724291-49724341	GM12878	blood:	n/a
8	chr3:49724291-49724341	AG04450	lung:	fetal
9	chr3:49724291-49724341	GM12891	blood:	n/a
10	chr3:49724291-49724341	Hela-S3	cervix:	n/a
11	chr3:49724291-49724341	K562	blood:	n/a
12	chr3:49724291-49724341	GM12892	blood:	n/a
13	chr3:49724291-49724341	ProgFib	skin:	n/a
14	chr3:49724291-49724341	A549	lung:	n/a
15	chr3:49724291-49724341	HEEpiC	esophagus:	n/a
16	chr3:49724291-49724341	NHBE	bronchial:	n/a
17	chr3:49724291-49724341	HNPCEpiC	eye:	n/a
18	chr3:49724291-49724341	LNCaP	prostate:	n/a
19	chr3:49724291-49724341	HRE	kidney:	n/a
20	chr3:49724291-49724341	HCT-116	colon:	n/a
21	chr3:49724291-49724341	CMK	blood:	n/a
22	chr3:49724291-49724341	HIPEpiC	eye:	n/a
23	chr3:49724291-49724341	HRCEpiC	kidney:	n/a
24	chr3:49724291-49724341	HMEC	breast:	n/a
25	chr3:49724291-49724341	BE2_C	brain:	n/a
26	chr3:49724291-49724341	SAEC	small airway:	n/a
27	chr3:49724291-49724341	MCF10A-Er-Src	breast:	n/a
28	chr3:49724291-49724341	GM06990	blood:	n/a
29	chr3:49724291-49724341	H1-hESC	embryonic stem cell:	embryo
30	chr3:49724291-49724341	U87	brain:	n/a
31	chr3:49724291-49724341	T-47D	breast:	n/a
32	chr3:49724291-49724341	ovcar-3	ovarian:	n/a
33	chr3:49724291-49724341	NT2-D1	testis:	n/a
34	chr3:49724291-49724341	IMR90	lung:	fetal
35	chr3:49724291-49724341	MCF-7	breast:	n/a
36	chr3:49724291-49724341	RPTEC	kidney:	n/a
37	chr3:49724291-49724341	BJ	skin:	n/a
38	chr3:49724291-49724341	SKMC	muscle:	n/a
39	chr3:49724291-49724341	NB4	blood:	n/a
40	chr3:49724291-49724341	GM19239	blood:	n/a
41	chr3:49724291-49724341	PFSK-1	brain:	n/a
42	chr3:49724291-49724341	AG10803	skin:	n/a
43	chr3:49724291-49724341	Jurkat	blood:	n/a
44	chr3:49724291-49724341	PANC-1	pancreas:	n/a
45	chr3:49724291-49724341	HEK293	kidney:	embryo
46	chr3:49724291-49724341	AG09309	skin:	n/a
47	chr3:49724291-49724341	HCF	heart:	n/a
48	chr3:49724291-49724341	HL-60	blood:	n/a
49	chr3:49724291-49724341	AG09319	gingival:	n/a
50	chr3:49724291-49724341	AoSMC	blood vessel:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr3:49715211..49719699-chr3:49722366..49724649,4	K562	blood:
2	chr3:49710552..49715225-chr3:49718907..49727364,14	MCF-7	breast:
3	chr1:17086818..17089262-chr3:49723617..49726310,2	MCF-7	breast:
4	chr3:49711727..49717769-chr3:49722772..49726950,7	K562	blood:
5	chr1:16964923..16974624-chr3:49722461..49732046,16	K562	blood:
6	chr3:49720877..49722933-chr3:49723247..49725096,3	K562	blood:
7	chr3:49719726..49722448-chr3:49723596..49725872,2	K562	blood:
8	chr3:49448668..49451033-chr3:49723995..49726731,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNF123	TF binding region
ENSG00000259970	TF binding region
MST1	TF binding region
ENSG00000259970	CpG island
RNF123	CpG island
MST1	CpG island
ENSG00000173531	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000186715	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000259970	Chromatin interaction
ENSG00000215908	Chromatin interaction
ENSG00000186301	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs34379671	1.00[AMR][1000 genomes]
rs34630302	1.00[AMR][1000 genomes]
rs35481257	1.00[AMR][1000 genomes]
rs6772424	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6777731	1.00[AMR][1000 genomes]
rs6797615	1.00[AMR][1000 genomes]
rs6800591	1.00[AMR][1000 genomes]
rs6806073	1.00[AMR][1000 genomes]
rs6808633	1.00[AMR][1000 genomes]
rs72938200	1.00[AMR][1000 genomes]
rs7615240	1.00[AMR][1000 genomes]
rs7616171	1.00[AMR][1000 genomes]
rs7623582	1.00[AMR][1000 genomes]
rs7626820	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7633189	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7634945	1.00[AMR][1000 genomes]
rs7636222	1.00[AMR][1000 genomes]
rs7637266	1.00[AMR][1000 genomes]
rs7648632	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv820990	chr3:49720651-49735911	Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv12377	chr3:49720751-49735851	Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	esv11877	chr3:49721171-49727086	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	nsv471425	chr3:49721381-49726196	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
9	nsv482080	chr3:49721381-49726196	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	nsv822077	chr3:49721400-49734526	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	esv1825475	chr3:49722732-49734243	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49712800-49726200	Weak transcription	Small Intestine	intestine
2	chr3:49719000-49726200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:49719800-49724400	Weak transcription	NHDF-Ad	bronchial
4	chr3:49720600-49726200	Weak transcription	A549	lung
5	chr3:49721000-49726200	Weak transcription	HSMM	muscle
6	chr3:49721400-49724400	Weak transcription	Brain Angular Gyrus	brain
7	chr3:49721400-49725800	Weak transcription	Hela-S3	cervix
8	chr3:49721400-49725800	Weak transcription	K562	blood
9	chr3:49721400-49726400	Weak transcription	Aorta	Aorta
10	chr3:49721600-49726200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:49722000-49724600	Weak transcription	Brain Anterior Caudate	brain
12	chr3:49722000-49724600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:49722400-49726200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:49723000-49724400	Active TSS	Pancreas	Pancrea
15	chr3:49723000-49724600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:49723000-49724600	Active TSS	Fetal Kidney	kidney
17	chr3:49723000-49725000	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr3:49723200-49724400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr3:49723200-49724400	Enhancers	Psoas Muscle	Psoas
20	chr3:49723200-49724600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:49723200-49724600	Active TSS	Duodenum Mucosa	Duodenum
22	chr3:49723200-49724800	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr3:49723200-49724800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr3:49723200-49724800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
25	chr3:49723200-49724800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
26	chr3:49723200-49725000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr3:49723200-49725000	Active TSS	H9 Cell Line	embryonic stem cell
28	chr3:49723200-49725000	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr3:49723200-49725600	Weak transcription	Dnd41	blood
30	chr3:49723400-49724400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr3:49723400-49724400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
32	chr3:49723400-49724400	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr3:49723400-49724400	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr3:49723400-49724400	Weak transcription	HepG2	liver
35	chr3:49723400-49724600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:49723400-49724600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:49723400-49725000	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr3:49723400-49725000	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr3:49723400-49725000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:49723400-49725200	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr3:49723400-49725800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:49723400-49725800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:49723400-49726400	Weak transcription	Lung	lung
44	chr3:49723600-49724600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
45	chr3:49723600-49724800	Enhancers	Primary B cells from cord blood	blood
46	chr3:49723800-49724400	Active TSS	Primary hematopoietic stem cells	blood
47	chr3:49723800-49724400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
48	chr3:49723800-49724400	Enhancers	GM12878-XiMat	blood
49	chr3:49723800-49724600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
50	chr3:49723800-49724600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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