Variant report

Variant	rs541361531
Chromosome Location	chr22:30685881-30685882
allele	G/T
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	TCF3	chr22:30685757-30686033	GM12878	blood:	n/a	n/a
2	POLR2A	chr22:30685164-30685987	K562	blood:	n/a	n/a
3	POLR2A	chr22:30685723-30686994	GM12878	blood:	n/a	n/a
4	POLR2A	chr22:30685314-30686056	HCT-116	colon:	n/a	n/a
5	NFATC1	chr22:30685373-30686098	GM12878	blood:	n/a	chr22:30685853-30685866
6	PML	chr22:30685241-30686822	GM12878	blood:	n/a	chr22:30685671-30685679
7	PAX5	chr22:30685274-30685920	GM12878	blood:	n/a	chr22:30685689-30685698
8	SP1	chr22:30685359-30685991	HepG2	liver:	n/a	chr22:30685790-30685802 chr22:30685815-30685827 chr22:30685816-30685826 chr22:30685537-30685546 chr22:30685815-30685827 chr22:30685816-30685826 chr22:30685536-30685548 chr22:30685834-30685847 chr22:30685536-30685548 chr22:30685817-30685826 chr22:30685538-30685547 chr22:30685816-30685825 chr22:30685816-30685825 chr22:30685655-30685665 chr22:30685844-30685856
9	CTCF	chr22:30685880-30686030	HCM	heart:	n/a	n/a
10	YY1	chr22:30685764-30686171	GM12878	blood:	n/a	chr22:30686095-30686106
11	USF1	chr22:30685496-30686044	SK-N-SH_RA	brain:	n/a	chr22:30685621-30685637
12	MAX	chr22:30685232-30686081	ECC-1	luminal epithelium:	n/a	chr22:30685833-30685843
13	IRF1	chr22:30685361-30686018	K562	blood:	n/a	chr22:30685652-30685666 chr22:30685842-30685856 chr22:30685667-30685676 chr22:30685686-30685700 chr22:30685536-30685550 chr22:30685813-30685827
14	POLR2A	chr22:30685235-30687312	GM12878	blood:	n/a	n/a
15	STAT1	chr22:30685438-30686026	GM12878	blood:	n/a	n/a
16	SP1	chr22:30685284-30686039	A549	lung:	n/a	chr22:30685790-30685802 chr22:30685815-30685827 chr22:30685816-30685826 chr22:30685537-30685546 chr22:30685815-30685827 chr22:30685816-30685826 chr22:30685536-30685548 chr22:30685834-30685847 chr22:30685536-30685548 chr22:30685817-30685826 chr22:30685538-30685547 chr22:30685816-30685825 chr22:30685816-30685825 chr22:30685655-30685665 chr22:30685844-30685856
17	NRF1	chr22:30685755-30686039	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr22:30685801-30686143	GM12891	blood:	n/a	n/a
19	SP4	chr22:30685407-30685949	H1-hESC	embryonic stem cell:	n/a	chr22:30685813-30685829
20	MAX	chr22:30685809-30686000	K562	blood:	n/a	chr22:30685833-30685843
21	POLR2A	chr22:30685366-30688017	GM12892	blood:	n/a	n/a
22	RUNX3	chr22:30685267-30685885	GM12878	blood:	n/a	n/a
23	MAX	chr22:30685224-30686161	A549	lung:	n/a	chr22:30685833-30685843
24	MAX	chr22:30685344-30686044	K562	blood:	n/a	chr22:30685833-30685843
25	POLR2A	chr22:30685244-30685932	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr22:30685222-30685898	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr22:30685344-30687144	GM12878	blood:	n/a	n/a
28	CTCF	chr22:30685570-30686115	GM12878	blood:	n/a	chr22:30686088-30686101
29	BHLHE40	chr22:30685448-30685938	GM12878	blood:	n/a	chr22:30685621-30685637
30	HMGN3	chr22:30684909-30686005	K562	blood:	n/a	n/a
31	POLR2A	chr22:30685268-30686959	GM18951	blood:	n/a	n/a
32	CCNT2	chr22:30685318-30685922	K562	blood:	n/a	chr22:30685817-30685826
33	NRF1	chr22:30685811-30685947	K562	blood:	n/a	n/a
34	POLR2A	chr22:30685211-30685961	HUVEC	blood vessel:	n/a	n/a
35	YY1	chr22:30685086-30686214	HepG2	liver:	n/a	chr22:30685545-30685554 chr22:30685252-30685263 chr22:30685543-30685554 chr22:30686095-30686106 chr22:30685546-30685557 chr22:30685581-30685592 chr22:30685219-30685238
36	MYC	chr22:30685866-30685945	HepG2	liver:	n/a	n/a
37	NFATC1	chr22:30685265-30686335	GM12878	blood:	n/a	chr22:30685853-30685866
38	POLR2A	chr22:30685788-30685899	A549	lung:	n/a	n/a
39	MAZ	chr22:30685432-30686121	HepG2	liver:	n/a	chr22:30685833-30685843
40	POLR2A	chr22:30685098-30686646	H1-hESC	embryonic stem cell:	n/a	n/a
41	RCOR1	chr22:30685285-30686404	GM12878	blood:	n/a	n/a
42	BCL3	chr22:30685237-30686243	GM12878	blood:	n/a	chr22:30685602-30685615 chr22:30685546-30685555 chr22:30685541-30685554 chr22:30685543-30685552 chr22:30685260-30685273 chr22:30685580-30685593 chr22:30685254-30685267 chr22:30685598-30685611
43	POLR2A	chr22:30685186-30686444	PFSK-1	brain:	n/a	n/a
44	POLR2A	chr22:30685195-30686178	HUVEC	blood vessel:	n/a	n/a
45	MAX	chr22:30685192-30686158	MCF-7	breast:	n/a	chr22:30685833-30685843
46	SP1	chr22:30685319-30686047	H1-hESC	embryonic stem cell:	n/a	chr22:30685790-30685802 chr22:30685815-30685827 chr22:30685816-30685826 chr22:30685537-30685546 chr22:30685815-30685827 chr22:30685816-30685826 chr22:30685536-30685548 chr22:30685834-30685847 chr22:30685536-30685548 chr22:30685817-30685826 chr22:30685538-30685547 chr22:30685816-30685825 chr22:30685816-30685825 chr22:30685655-30685665 chr22:30685844-30685856
47	ZBTB7A	chr22:30684611-30685906	K562	blood:	n/a	chr22:30685829-30685838
48	POLR2A	chr22:30685291-30687284	GM12892	blood:	n/a	n/a
49	POLR2A	chr22:30685327-30687530	GM18505	blood:	n/a	n/a
50	PBX3	chr22:30685320-30686020	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:30684944..30687538-chr22:30739118..30741799,2	MCF-7	breast:
2	chr22:30684284..30686749-chr22:30752450..30754272,3	MCF-7	breast:
3	chr22:30684150..30686115-chr22:30783000..30785215,3	K562	blood:
4	chr22:30681692..30688141-chr22:30720232..30725114,19	MCF-7	breast:
5	chr22:30685629..30687266-chr22:30839148..30841021,2	K562	blood:
6	chr22:30679588..30687274-chr22:30748772..30756086,11	MCF-7	breast:
7	chr22:30681129..30691076-chr22:30751303..30759078,14	K562	blood:
8	chr22:30683198..30686724-chr22:30818649..30821641,4	K562	blood:
9	chr22:30683831..30686273-chr22:30722432..30724567,2	K562	blood:
10	chr22:30684219..30686932-chr22:30699973..30702656,2	MCF-7	breast:
11	chr22:30683076..30686857-chr22:30780059..30784684,12	MCF-7	breast:
12	chr22:30684393..30686613-chr22:30820961..30823363,3	MCF-7	breast:

Variant related genes	Relation type
GATSL3	TF binding region
ENSG00000099999	Chromatin interaction
ENSG00000099992	Chromatin interaction
ENSG00000242114	Chromatin interaction
ENSG00000187860	Chromatin interaction
ENSG00000099995	Chromatin interaction

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

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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	esv1799458	chr22:30659798-30698035	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv588885	chr22:30661184-30691631	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv522605	chr22:30685076-30691631	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30683600-30686800	Flanking Active TSS	Dnd41	blood
2	chr22:30683800-30686000	Active TSS	Fetal Kidney	kidney
3	chr22:30684000-30686000	Active TSS	Brain Anterior Caudate	brain
4	chr22:30684000-30686400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr22:30684000-30686600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr22:30684200-30686000	Active TSS	Right Atrium	heart
7	chr22:30684200-30686200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr22:30684200-30686200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr22:30684200-30686200	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr22:30684200-30686200	Active TSS	Brain Angular Gyrus	brain
11	chr22:30684200-30686200	Enhancers	Fetal Brain Male	brain
12	chr22:30684200-30686200	Active TSS	Ovary	ovary
13	chr22:30684400-30686000	Active TSS	Brain Substantia Nigra	brain
14	chr22:30684400-30686000	Active TSS	Left Ventricle	heart
15	chr22:30684400-30686200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr22:30684400-30686200	Active TSS	Aorta	Aorta
17	chr22:30684400-30686200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr22:30684600-30686000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr22:30684600-30686000	Active TSS	A549	lung
20	chr22:30684600-30686200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr22:30684600-30686200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr22:30684600-30686200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr22:30684600-30686200	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr22:30684600-30686200	Active TSS	Small Intestine	intestine
25	chr22:30684600-30686400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr22:30684800-30686000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr22:30684800-30686000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr22:30684800-30686000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr22:30684800-30686000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr22:30684800-30686000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr22:30684800-30686000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr22:30684800-30686000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr22:30684800-30686000	Active TSS	Colon Smooth Muscle	Colon
34	chr22:30684800-30686000	Active TSS	Esophagus	oesophagus
35	chr22:30684800-30686000	Active TSS	Rectal Smooth Muscle	rectum
36	chr22:30684800-30686000	Active TSS	NHLF	lung
37	chr22:30684800-30686200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr22:30684800-30686200	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr22:30684800-30686200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr22:30684800-30686200	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr22:30684800-30686400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr22:30685000-30686000	Active TSS	H1 Cell Line	embryonic stem cell
43	chr22:30685000-30686000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr22:30685000-30686000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr22:30685000-30686000	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr22:30685000-30686000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr22:30685000-30686000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr22:30685000-30686000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr22:30685000-30686000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr22:30685000-30686000	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links