Variant report

Variant	rs3761427
Chromosome Location	chr22:30644826-30644827
allele	C/G
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	POLR2A	chr22:30642907-30646562	HCT-116	colon:	n/a	n/a
2	POLR2A	chr22:30634332-30646592	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr22:30644823-30645023	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr22:30643828-30645616	A549	lung:	n/a	n/a
5	MAZ	chr22:30644457-30650761	IMR90	lung:	n/a	chr22:30646776-30646786 chr22:30646530-30646540 chr22:30644558-30644569 chr22:30649241-30649251
6	POLR2A	chr22:30631062-30645095	IMR90	lung:	n/a	n/a
7	MAX	chr22:30643129-30645971	A549	lung:	n/a	chr22:30644558-30644569
8	POLR2A	chr22:30633461-30651267	A549	lung:	n/a	n/a
9	POLR2A	chr22:30640309-30646586	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr22:30639359-30648158	MCF-7	breast:	n/a	n/a
11	POLR2A	chr22:30644736-30645204	A549	lung:	n/a	n/a
12	SPI1	chr22:30644794-30644968	K562	blood:	n/a	chr22:30644890-30644903 chr22:30644890-30644903 chr22:30644891-30644904 chr22:30644893-30644902
13	POLR2A	chr22:30643916-30644883	A549	lung:	n/a	n/a
14	ELF1	chr22:30644775-30644996	K562	blood:	n/a	chr22:30644891-30644902 chr22:30644890-30644903 chr22:30644892-30644903
15	POLR2A	chr22:30634469-30646541	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:30578823..30581368-chr22:30643689..30645542,2	MCF-7	breast:
2	chr22:30641395..30644994-chr22:30815782..30819866,5	MCF-7	breast:
3	chr22:30500122..30506829-chr22:30640771..30648697,14	MCF-7	breast:
4	chr13:38448816..38451561-chr22:30643041..30645856,2	MCF-7	breast:
5	chr22:30644640..30647601-chr22:30649599..30653235,3	K562	blood:
6	chr22:30642799..30644915-chr22:30699451..30702374,2	MCF-7	breast:

Variant related genes	Relation type
LIF	TF binding region
ENSG00000273350	Chromatin interaction
ENSG00000226573	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000272689	Chromatin interaction
ENSG00000099992	Chromatin interaction
ENSG00000222915	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11089441	0.86[CEU][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13054238	0.84[AFR][1000 genomes]
rs2267153	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3753082	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs929271	0.86[CHB][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs929273	0.91[CHB][hapmap]
rs9606708	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv432239	chr22:30580161-30669883	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv914968	chr22:30610570-30693581	Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv914969	chr22:30619599-30691631	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription 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	51 gene(s)	inside rSNPs	diseases
7	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv914971	chr22:30640308-30691631	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv914972	chr22:30640308-30693581	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30632600-30645200	Weak transcription	Hela-S3	cervix
2	chr22:30634000-30646800	Genic enhancers	A549	lung
3	chr22:30642800-30645000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr22:30642800-30645000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr22:30642800-30645000	Weak transcription	Ovary	ovary
6	chr22:30642800-30645200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr22:30642800-30645600	Enhancers	Gastric	stomach
8	chr22:30642800-30646400	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr22:30642800-30648800	Weak transcription	Right Atrium	heart
10	chr22:30643000-30645200	Enhancers	Primary hematopoietic stem cells	blood
11	chr22:30643000-30645200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr22:30643200-30645000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr22:30643200-30645200	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr22:30643200-30645200	Flanking Active TSS	HSMMtube	muscle
15	chr22:30643200-30645600	Flanking Active TSS	HepG2	liver
16	chr22:30643200-30647000	Weak transcription	Pancreas	Pancrea
17	chr22:30643200-30649000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr22:30643200-30651000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr22:30643400-30645600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr22:30643400-30645800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr22:30643400-30647400	Weak transcription	Lung	lung
22	chr22:30643400-30648400	Weak transcription	Esophagus	oesophagus
23	chr22:30643400-30649200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr22:30643600-30645000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr22:30643600-30645000	Enhancers	Dnd41	blood
26	chr22:30643600-30645800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr22:30643600-30647000	Enhancers	Fetal Intestine Large	intestine
28	chr22:30643600-30647400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr22:30643600-30648000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr22:30643600-30648000	Weak transcription	Fetal Brain Female	brain
31	chr22:30643600-30648800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr22:30643600-30649800	Enhancers	HMEC	breast
33	chr22:30643600-30650800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr22:30643600-30658400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr22:30643800-30645000	Weak transcription	NHDF-Ad	bronchial
36	chr22:30643800-30645400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr22:30643800-30646000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr22:30643800-30647200	Weak transcription	GM12878-XiMat	blood
39	chr22:30643800-30648400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr22:30643800-30649000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr22:30643800-30650000	Enhancers	Osteobl	bone
42	chr22:30643800-30651000	Enhancers	NH-A	brain
43	chr22:30644000-30645200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
44	chr22:30644000-30645400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr22:30644000-30645400	Enhancers	Small Intestine	intestine
46	chr22:30644000-30645400	Enhancers	Spleen	Spleen
47	chr22:30644000-30646400	Enhancers	Duodenum Mucosa	Duodenum
48	chr22:30644200-30645200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr22:30644200-30645200	Flanking Active TSS	HSMM	muscle
50	chr22:30644200-30645400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links