Variant report

Variant	rs9606708
Chromosome Location	chr22:30646126-30646127
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	POLR2A	chr22:30642907-30646562	HCT-116	colon:	n/a	n/a
2	EP300	chr22:30645911-30650592	ECC-1	luminal epithelium:	n/a	chr22:30650501-30650508 chr22:30648788-30648797 chr22:30649040-30649050 chr22:30647931-30647945
3	POLR2A	chr22:30645300-30650267	IMR90	lung:	n/a	n/a
4	POLR2A	chr22:30634332-30646592	PANC-1	pancreas:	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	chr22:30646048-30646598	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr22:30633461-30651267	A549	lung:	n/a	n/a
8	POLR2A	chr22:30640309-30646586	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr22:30639359-30648158	MCF-7	breast:	n/a	n/a
10	NFIC	chr22:30645950-30650198	ECC-1	luminal epithelium:	n/a	chr22:30647836-30647853 chr22:30649459-30649476 chr22:30649459-30649475
11	NFIC	chr22:30646047-30648191	ECC-1	luminal epithelium:	n/a	chr22:30647836-30647853
12	TCF12	chr22:30646072-30647962	ECC-1	luminal epithelium:	n/a	chr22:30647573-30647583 chr22:30646719-30646729
13	TCF12	chr22:30645883-30647548	ECC-1	luminal epithelium:	n/a	chr22:30646719-30646729
14	POLR2A	chr22:30634469-30646541	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:30491317..30493924-chr22:30645832..30648573,3	MCF-7	breast:
2	chr22:30645897..30647420-chr22:30816892..30819788,2	MCF-7	breast:
3	chr22:30500122..30506829-chr22:30640771..30648697,14	MCF-7	breast:
4	chr22:30505986..30512409-chr22:30645938..30650817,6	MCF-7	breast:
5	chr22:30644640..30647601-chr22:30649599..30653235,3	K562	blood:

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

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11089441	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13054238	0.84[AFR][1000 genomes]
rs2267153	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3753082	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3761427	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]
rs929271	0.89[ASW][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.91[MEX][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs929273	0.91[CHB][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9606708	RNF185	cis	cerebellum	SCAN
rs9606708	C22orf42	cis	cerebellum	SCAN
rs9606708	SYN3	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30634000-30646800	Genic enhancers	A549	lung
2	chr22:30642800-30646400	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr22:30642800-30648800	Weak transcription	Right Atrium	heart
4	chr22:30643200-30647000	Weak transcription	Pancreas	Pancrea
5	chr22:30643200-30649000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr22:30643200-30651000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:30643400-30647400	Weak transcription	Lung	lung
8	chr22:30643400-30648400	Weak transcription	Esophagus	oesophagus
9	chr22:30643400-30649200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr22:30643600-30647000	Enhancers	Fetal Intestine Large	intestine
11	chr22:30643600-30647400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr22:30643600-30648000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr22:30643600-30648000	Weak transcription	Fetal Brain Female	brain
14	chr22:30643600-30648800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr22:30643600-30649800	Enhancers	HMEC	breast
16	chr22:30643600-30650800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr22:30643600-30658400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr22:30643800-30647200	Weak transcription	GM12878-XiMat	blood
19	chr22:30643800-30648400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr22:30643800-30649000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr22:30643800-30650000	Enhancers	Osteobl	bone
22	chr22:30643800-30651000	Enhancers	NH-A	brain
23	chr22:30644000-30646400	Enhancers	Duodenum Mucosa	Duodenum
24	chr22:30644200-30647400	Weak transcription	Fetal Brain Male	brain
25	chr22:30644400-30647600	Bivalent Enhancer	Placenta	Placenta
26	chr22:30644600-30646600	Weak transcription	Primary B cells from cord blood	blood
27	chr22:30644600-30652000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr22:30644800-30646200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr22:30644800-30646200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr22:30644800-30646400	Enhancers	Right Ventricle	heart
31	chr22:30644800-30651600	Genic enhancers	Fetal Intestine Small	intestine
32	chr22:30645000-30648800	Weak transcription	Dnd41	blood
33	chr22:30645000-30650200	Enhancers	NHDF-Ad	bronchial
34	chr22:30645200-30646200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr22:30645200-30648600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr22:30645200-30648600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr22:30645200-30648600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr22:30645200-30648600	Weak transcription	Left Ventricle	heart
39	chr22:30645200-30648600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr22:30645200-30648800	Enhancers	Hela-S3	cervix
41	chr22:30645200-30648800	Enhancers	NHLF	lung
42	chr22:30645200-30650800	Enhancers	HSMM	muscle
43	chr22:30645200-30651000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr22:30645200-30652000	Enhancers	HSMMtube	muscle
45	chr22:30645400-30646200	Weak transcription	Stomach Mucosa	stomach
46	chr22:30645400-30646400	Enhancers	Fetal Kidney	kidney
47	chr22:30645400-30646800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr22:30645400-30646800	Enhancers	Fetal Stomach	stomach
49	chr22:30645400-30646800	Weak transcription	Small Intestine	intestine
50	chr22:30645400-30647000	Weak transcription	Spleen	Spleen

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