Variant report

Variant	rs6006417
Chromosome Location	chr22:30647657-30647658
allele	C/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	BCL3	chr22:30647579-30648076	A549	lung:	n/a	n/a
2	NFIC	chr22:30647553-30648126	SK-N-SH	brain:	n/a	chr22:30647836-30647853
3	EP300	chr22:30645911-30650592	ECC-1	luminal epithelium:	n/a	chr22:30650501-30650508 chr22:30648788-30648797 chr22:30649040-30649050 chr22:30647931-30647945
4	POLR2A	chr22:30645300-30650267	IMR90	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	MAX	chr22:30646165-30650067	A549	lung:	n/a	chr22:30646776-30646786 chr22:30646530-30646540 chr22:30649241-30649251
7	EP300	chr22:30647631-30648104	SK-N-SH_RA	brain:	n/a	chr22:30647931-30647945
8	EP300	chr22:30647610-30648067	SK-N-SH_RA	brain:	n/a	chr22:30647931-30647945
9	POLR2A	chr22:30647465-30647863	A549	lung:	n/a	n/a
10	POLR2A	chr22:30646676-30650172	ECC-1	luminal epithelium:	n/a	n/a
11	SP1	chr22:30647655-30648175	A549	lung:	n/a	n/a
12	POLR2A	chr22:30633461-30651267	A549	lung:	n/a	n/a
13	TCF12	chr22:30647560-30648227	SK-N-SH	brain:	n/a	chr22:30647573-30647583
14	POLR2A	chr22:30647178-30650178	HCT-116	colon:	n/a	n/a
15	POLR2A	chr22:30639359-30648158	MCF-7	breast:	n/a	n/a
16	NFIC	chr22:30645950-30650198	ECC-1	luminal epithelium:	n/a	chr22:30647836-30647853 chr22:30649459-30649476 chr22:30649459-30649475
17	JUND	chr22:30647427-30648086	A549	lung:	n/a	n/a
18	NFIC	chr22:30647468-30648281	SK-N-SH	brain:	n/a	chr22:30647836-30647853
19	NFIC	chr22:30646047-30648191	ECC-1	luminal epithelium:	n/a	chr22:30647836-30647853
20	ZBTB7A	chr22:30646435-30647667	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr22:30646679-30649339	PANC-1	pancreas:	n/a	n/a
22	STAT3	chr22:30647618-30648128	MCF10A-Er-Src	breast:	n/a	n/a
23	TCF12	chr22:30646742-30650060	A549	lung:	n/a	chr22:30649397-30649404 chr22:30647573-30647583
24	POLR2A	chr22:30646672-30651442	HCT-116	colon:	n/a	n/a
25	FOSL2	chr22:30647547-30648119	A549	lung:	n/a	n/a
26	TCF12	chr22:30646072-30647962	ECC-1	luminal epithelium:	n/a	chr22:30647573-30647583 chr22:30646719-30646729
27	POLR2A	chr22:30646719-30647885	ECC-1	luminal epithelium:	n/a	n/a
28	PBX3	chr22:30647540-30648256	SK-N-SH	brain:	n/a	chr22:30647739-30647759
29	PBX3	chr22:30647593-30648135	SK-N-SH	brain:	n/a	chr22:30647739-30647759
30	ZBTB7A	chr22:30646145-30647793	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:30491317..30493924-chr22:30645832..30648573,3	MCF-7	breast:
2	chr22:30647267..30649717-chr22:30990024..30992497,2	MCF-7	breast:
3	chr22:30510449..30512616-chr22:30646974..30649520,2	MCF-7	breast:
4	chr22:30647437..30649657-chr22:30691811..30694228,2	MCF-7	breast:
5	chr22:30647129..30650015-chr22:30704235..30707328,3	MCF-7	breast:
6	chr2:242403187..242406087-chr22:30646578..30648381,2	MCF-7	breast:
7	chr22:30500122..30506829-chr22:30640771..30648697,14	MCF-7	breast:
8	chr22:30505986..30512409-chr22:30645938..30650817,6	MCF-7	breast:

Variant related genes	Relation type
LIF	TF binding region
ENSG00000226573	Chromatin interaction
ENSG00000099992	Chromatin interaction
ENSG00000248751	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12166309	1.00[EUR][1000 genomes]
rs12169153	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16988421	1.00[EUR][1000 genomes]
rs16988425	1.00[EUR][1000 genomes]
rs16988643	1.00[CEU][hapmap]
rs56897799	1.00[EUR][1000 genomes]
rs5997599	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6006413	1.00[EUR][1000 genomes]
rs60836642	1.00[EUR][1000 genomes]
rs61732271	1.00[EUR][1000 genomes]
rs7286437	1.00[EUR][1000 genomes]
rs7291157	1.00[EUR][1000 genomes]
rs73404556	1.00[EUR][1000 genomes]
rs73881424	1.00[EUR][1000 genomes]
rs73883356	1.00[EUR][1000 genomes]
rs8142884	1.00[EUR][1000 genomes]
rs9614164	1.00[JPT][hapmap]
rs9619095	1.00[ASN][1000 genomes]
rs9620963	1.00[ASN][1000 genomes]
rs9620975	1.00[EUR][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:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30642800-30648800	Weak transcription	Right Atrium	heart
2	chr22:30643200-30649000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr22:30643200-30651000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:30643400-30648400	Weak transcription	Esophagus	oesophagus
5	chr22:30643400-30649200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr22:30643600-30648000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr22:30643600-30648000	Weak transcription	Fetal Brain Female	brain
8	chr22:30643600-30648800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr22:30643600-30649800	Enhancers	HMEC	breast
10	chr22:30643600-30650800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr22:30643600-30658400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr22:30643800-30648400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr22:30643800-30649000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr22:30643800-30650000	Enhancers	Osteobl	bone
15	chr22:30643800-30651000	Enhancers	NH-A	brain
16	chr22:30644600-30652000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr22:30644800-30651600	Genic enhancers	Fetal Intestine Small	intestine
18	chr22:30645000-30648800	Weak transcription	Dnd41	blood
19	chr22:30645000-30650200	Enhancers	NHDF-Ad	bronchial
20	chr22:30645200-30648600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr22:30645200-30648600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr22:30645200-30648600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr22:30645200-30648600	Weak transcription	Left Ventricle	heart
24	chr22:30645200-30648600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr22:30645200-30648800	Enhancers	Hela-S3	cervix
26	chr22:30645200-30648800	Enhancers	NHLF	lung
27	chr22:30645200-30650800	Enhancers	HSMM	muscle
28	chr22:30645200-30651000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr22:30645200-30652000	Enhancers	HSMMtube	muscle
30	chr22:30645400-30648600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr22:30645400-30650000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr22:30645400-30651400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr22:30645600-30648200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr22:30645600-30648200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr22:30645600-30648600	Weak transcription	Fetal Thymus	thymus
36	chr22:30645600-30648600	Weak transcription	Gastric	stomach
37	chr22:30645600-30648800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr22:30645600-30648800	Weak transcription	Colonic Mucosa	Colon
39	chr22:30645600-30649000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr22:30645800-30648000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr22:30646000-30648400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr22:30646000-30650200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr22:30646200-30648000	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr22:30646200-30649600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr22:30646200-30649800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr22:30646400-30648000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr22:30646400-30648600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr22:30646400-30648600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr22:30646400-30648800	Weak transcription	Fetal Kidney	kidney
50	chr22:30646400-30649800	Enhancers	NHEK	skin

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