Variant report

Variant	rs3813879
Chromosome Location	chr11:3875982-3875983
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr11:3875089-3876771	GM10847	blood:	n/a	n/a
2	BCLAF1	chr11:3875484-3876668	GM12878	blood:	n/a	n/a
3	MAX	chr11:3875678-3876549	K562	blood:	n/a	n/a
4	POLR2A	chr11:3875307-3876592	GM12892	blood:	n/a	n/a
5	JUND	chr11:3875927-3876562	H1-hESC	embryonic stem cell:	n/a	chr11:3876024-3876033
6	NFIC	chr11:3875105-3876559	GM12878	blood:	n/a	n/a
7	STAT1	chr11:3875619-3877099	GM12878	blood:	n/a	chr11:3875906-3875914 chr11:3876019-3876031
8	TAF1	chr11:3875647-3876587	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr11:3875966-3876814	ECC-1	luminal epithelium:	n/a	n/a
10	SP1	chr11:3875882-3876465	H1-hESC	embryonic stem cell:	n/a	chr11:3876024-3876036 chr11:3876021-3876035 chr11:3876024-3876036 chr11:3876025-3876035 chr11:3876025-3876034 chr11:3876026-3876035
11	TCF12	chr11:3875594-3877673	A549	lung:	n/a	n/a
12	MAX	chr11:3875559-3877908	A549	lung:	n/a	chr11:3877019-3877029 chr11:3876969-3876979
13	POLR2A	chr11:3875304-3877670	GM19099	blood:	n/a	n/a
14	SP1	chr11:3875905-3876760	K562	blood:	n/a	chr11:3876024-3876036 chr11:3876021-3876035 chr11:3876024-3876036 chr11:3876025-3876035 chr11:3876025-3876034 chr11:3876026-3876035
15	POLR2A	chr11:3875197-3876762	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:3875980-3877253	U87	brain:	n/a	n/a
17	POLR2A	chr11:3875617-3877641	K562	blood:	n/a	n/a
18	SPI1	chr11:3875177-3875982	GM12891	blood:	n/a	n/a
19	CHD1	chr11:3875301-3876848	IMR90	lung:	n/a	n/a
20	MYC	chr11:3875130-3878021	K562	blood:	n/a	chr11:3877019-3877029 chr11:3876969-3876979
21	RCOR1	chr11:3874971-3876804	GM12878	blood:	n/a	n/a
22	RELA	chr11:3875154-3876639	GM18951	blood:	n/a	n/a
23	RELA	chr11:3875296-3876779	GM15510	blood:	n/a	n/a
24	MAX	chr11:3875918-3877737	HepG2	liver:	n/a	chr11:3877019-3877029 chr11:3876969-3876979
25	PAX5	chr11:3875641-3875997	GM12878	blood:	n/a	n/a
26	CREB1	chr11:3875245-3876669	GM12878	blood:	n/a	n/a
27	SIN3A	chr11:3875691-3877827	H1-hESC	embryonic stem cell:	n/a	chr11:3876896-3876909 chr11:3876978-3876991 chr11:3876791-3876804 chr11:3876778-3876789
28	MYC	chr11:3875752-3876488	MCF10A-Er-Src	breast:	n/a	n/a
29	RUNX3	chr11:3875081-3876862	GM12878	blood:	n/a	n/a
30	UBTF	chr11:3875741-3876770	K562	blood:	n/a	n/a
31	POLR2A	chr11:3875132-3876771	GM12892	blood:	n/a	n/a
32	POLR2A	chr11:3875929-3877341	PFSK-1	brain:	n/a	n/a
33	SP1	chr11:3875659-3876498	GM12878	blood:	n/a	chr11:3876024-3876036 chr11:3876021-3876035 chr11:3876024-3876036 chr11:3876025-3876035 chr11:3876025-3876034 chr11:3876026-3876035
34	CUX1	chr11:3875612-3876428	K562	blood:	n/a	n/a
35	PML	chr11:3875887-3876863	K562	blood:	n/a	n/a
36	POLR2A	chr11:3875629-3876700	K562	blood:	n/a	n/a
37	ZBTB7A	chr11:3875972-3876628	K562	blood:	n/a	n/a
38	SP1	chr11:3875811-3876642	H1-hESC	embryonic stem cell:	n/a	chr11:3876024-3876036 chr11:3876021-3876035 chr11:3876024-3876036 chr11:3876025-3876035 chr11:3876025-3876034 chr11:3876026-3876035
39	PML	chr11:3875542-3876060	GM12878	blood:	n/a	n/a
40	USF2	chr11:3875626-3876557	GM12878	blood:	n/a	n/a
41	CTCF	chr11:3875840-3875990	Hela-S3	cervix:	n/a	n/a
42	TAF1	chr11:3875592-3876036	GM12892	blood:	n/a	n/a
43	MYC	chr11:3875625-3877833	NB4	blood:	n/a	chr11:3877019-3877029 chr11:3876969-3876979
44	TFAP2C	chr11:3875944-3876772	Hela-S3	cervix:	n/a	n/a
45	YY1	chr11:3875595-3876789	GM12878	blood:	n/a	n/a
46	SMC3	chr11:3875419-3877786	SK-N-SH	brain:	n/a	chr11:3876926-3876936
47	POLR2A	chr11:3875470-3877773	K562	blood:	n/a	n/a
48	UBTF	chr11:3875656-3878155	K562	blood:	n/a	n/a
49	SP4	chr11:3875788-3876519	H1-hESC	embryonic stem cell:	n/a	n/a
50	CHD2	chr11:3875190-3876732	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:3858623..3864245-chr11:3874959..3879217,11	K562	blood:
2	chr11:3861906..3862744-chr11:3875851..3876670,2	K562	blood:
3	chr11:3861261..3864016-chr11:3874431..3876289,3	MCF-7	breast:
4	chr11:3816345..3819166-chr11:3875729..3878020,2	K562	blood:
5	chr11:3860189..3865275-chr11:3872883..3879283,10	K562	blood:

Variant related genes	Relation type
MIR4687	TF binding region
STIM1	TF binding region
ENSG00000177105	Chromatin interaction
ENSG00000110713	Chromatin interaction
ENSG00000148985	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10835184	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10835185	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835191	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835192	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11030054	0.91[ASN][1000 genomes]
rs12417801	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12421093	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12795081	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1869002	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813880	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910858	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7131058	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' 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	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1046325	chr11:3856201-3895148	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1039059	chr11:3856201-3909415	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv540910	chr11:3856201-3909415	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1051580	chr11:3856201-3924216	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1043265	chr11:3856201-3926407	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
13	nsv896894	chr11:3859856-3888234	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3874200-3876400	Weak transcription	Small Intestine	intestine
2	chr11:3874600-3876200	Enhancers	Placenta Amnion	Placenta Amnion
3	chr11:3874800-3876000	Enhancers	Fetal Muscle Leg	muscle
4	chr11:3874800-3876200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr11:3875000-3876000	Weak transcription	Psoas Muscle	Psoas
6	chr11:3875000-3876200	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr11:3875000-3876200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr11:3875000-3876200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr11:3875000-3876200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr11:3875200-3876000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:3875200-3876000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:3875200-3876000	Enhancers	Fetal Intestine Small	intestine
13	chr11:3875200-3876000	Enhancers	Pancreas	Pancrea
14	chr11:3875200-3876000	Enhancers	Spleen	Spleen
15	chr11:3875200-3876200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:3875200-3876200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:3875200-3876200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr11:3875200-3876200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr11:3875200-3876200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:3875200-3876200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr11:3875200-3876200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr11:3875200-3876200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr11:3875200-3876200	Enhancers	Placenta	Placenta
24	chr11:3875200-3876200	Enhancers	Stomach Mucosa	stomach
25	chr11:3875200-3876200	Flanking Active TSS	Dnd41	blood
26	chr11:3875200-3876200	Flanking Active TSS	GM12878-XiMat	blood
27	chr11:3875200-3876600	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr11:3875400-3876000	Enhancers	Fetal Stomach	stomach
29	chr11:3875400-3876200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr11:3875400-3876200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr11:3875400-3876200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr11:3875400-3876200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:3875400-3876200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:3875400-3876200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr11:3875400-3876200	Flanking Active TSS	Fetal Thymus	thymus
36	chr11:3875400-3876200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr11:3875400-3876200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr11:3875400-3876200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr11:3875400-3876200	Flanking Active TSS	HepG2	liver
40	chr11:3875400-3876200	Flanking Active TSS	K562	blood
41	chr11:3875400-3876200	Flanking Active TSS	NHEK	skin
42	chr11:3875400-3876400	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr11:3875400-3876400	Enhancers	NHDF-Ad	bronchial
44	chr11:3875600-3876000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:3875600-3876000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr11:3875600-3876000	Enhancers	Esophagus	oesophagus
47	chr11:3875600-3876000	Enhancers	Fetal Intestine Large	intestine
48	chr11:3875600-3876000	Enhancers	Right Atrium	heart
49	chr11:3875600-3876000	Enhancers	HSMM	muscle
50	chr11:3875600-3876000	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links