Variant report

Variant	rs1046199
Chromosome Location	chr22:30820550-30820551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:121)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:121 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr22:30819700-30820564	GM12878	blood:	n/a	n/a
2	EP300	chr22:30819704-30820683	K562	blood:	n/a	n/a
3	ATF2	chr22:30819638-30820714	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr22:30818691-30821114	HUVEC	blood vessel:	n/a	n/a
5	TCF12	chr22:30818644-30820552	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr22:30819325-30820611	A549	lung:	n/a	n/a
7	POLR2A	chr22:30818696-30821184	HUVEC	blood vessel:	n/a	n/a
8	E2F4	chr22:30819942-30820943	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr22:30817434-30821076	HUVEC	blood vessel:	n/a	n/a
10	TBP	chr22:30819680-30820915	K562	blood:	n/a	n/a
11	EP300	chr22:30819705-30820655	GM12878	blood:	n/a	n/a
12	MAX	chr22:30818767-30820600	HepG2	liver:	n/a	n/a
13	MAZ	chr22:30818156-30822979	IMR90	lung:	n/a	n/a
14	CTCF	chr22:30820460-30820610	SK-N-SH_RA	brain:	n/a	n/a
15	USF1	chr22:30819907-30820719	SK-N-SH	brain:	n/a	n/a
16	USF1	chr22:30819647-30820604	ECC-1	luminal epithelium:	n/a	n/a
17	JUND	chr22:30818641-30821043	HCT-116	colon:	n/a	chr22:30819046-30819057
18	JUND	chr22:30818669-30820679	HCT-116	colon:	n/a	chr22:30819046-30819057
19	POLR2A	chr22:30819204-30820812	GM12878	blood:	n/a	n/a
20	POLR2A	chr22:30816349-30821249	IMR90	lung:	n/a	n/a
21	POLR2A	chr22:30818871-30822893	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr22:30818645-30822915	Hela-S3	cervix:	n/a	n/a
23	USF1	chr22:30818733-30820599	HCT-116	colon:	n/a	n/a
24	POLR2A	chr22:30818456-30821082	GM12891	blood:	n/a	n/a
25	IRF3	chr22:30820043-30820674	HepG2	liver:	n/a	n/a
26	POLR2A	chr22:30817509-30822980	HUVEC	blood vessel:	n/a	n/a
27	ZNF143	chr22:30819651-30820731	GM12878	blood:	n/a	n/a
28	MYC	chr22:30818841-30820766	K562	blood:	n/a	n/a
29	STAT1	chr22:30819398-30820746	GM12878	blood:	n/a	n/a
30	CHD1	chr22:30816159-30822993	IMR90	lung:	n/a	n/a
31	POLR2A	chr22:30818198-30821196	GM12878	blood:	n/a	n/a
32	SIX5	chr22:30819146-30820615	A549	lung:	n/a	n/a
33	POLR2A	chr22:30818654-30821241	HCT-116	colon:	n/a	n/a
34	USF1	chr22:30819740-30820579	SK-N-SH	brain:	n/a	n/a
35	CTCF	chr22:30820540-30820690	NHLF	lung:	n/a	n/a
36	YY1	chr22:30819522-30820885	H1-hESC	embryonic stem cell:	n/a	chr22:30820038-30820058
37	CHD1	chr22:30818931-30820931	GM12878	blood:	n/a	n/a
38	POLR2A	chr22:30816245-30822974	PBDE	blood:	n/a	n/a
39	SP1	chr22:30817995-30821122	HCT-116	colon:	n/a	n/a
40	USF1	chr22:30819853-30820571	K562	blood:	n/a	n/a
41	POLR2A	chr22:30818136-30822953	HCT-116	colon:	n/a	n/a
42	POLR2A	chr22:30818744-30820605	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr22:30818761-30820850	HUVEC	blood vessel:	n/a	n/a
44	ZNF384	chr22:30820027-30820820	GM12878	blood:	n/a	n/a
45	POLR2A	chr22:30818514-30821189	GM12878	blood:	n/a	n/a
46	TAF1	chr22:30818827-30820568	K562	blood:	n/a	n/a
47	MAX	chr22:30818678-30820596	A549	lung:	n/a	n/a
48	POLR2A	chr22:30818991-30821080	GM19099	blood:	n/a	n/a
49	PBX3	chr22:30818682-30820582	SK-N-SH	brain:	n/a	n/a
50	RELA	chr22:30819662-30822768	GM18505	blood:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30814763..30819112-chr22:30819393..30823307,5	MCF-7	breast:
2	chr22:30820440..30822751-chr22:31090157..31092444,2	MCF-7	breast:
3	chr22:30683198..30686724-chr22:30818649..30821641,4	K562	blood:
4	chr22:30816361..30822733-chr22:30829064..30833429,8	K562	blood:
5	chr22:30818699..30820979-chr22:30839778..30841389,2	K562	blood:
6	chr22:30780643..30783306-chr22:30818763..30821068,2	MCF-7	breast:
7	chr22:30683198..30685731-chr22:30819153..30821641,4	K562	blood:
8	chr22:30819744..30820647-chr6:27860502..27861015,2	Hela-S3	cervix:
9	chr22:30722829..30724775-chr22:30819297..30822266,2	MCF-7	breast:
10	chr22:30791754..30798377-chr22:30814746..30822334,13	K562	blood:
11	chr22:30801331..30806439-chr22:30816907..30821751,5	K562	blood:
12	chr22:30647828..30650032-chr22:30818510..30820728,3	MCF-7	breast:
13	chr22:30661604..30663731-chr22:30819612..30821405,2	MCF-7	breast:
14	chr22:30502612..30504825-chr22:30819472..30821124,2	MCF-7	breast:
15	chr22:30783066..30785199-chr22:30819529..30822458,2	K562	blood:
16	chr22:30780810..30782737-chr22:30819771..30822166,2	MCF-7	breast:
17	chr22:30787731..30797808-chr22:30813672..30825727,31	MCF-7	breast:
18	chr22:30819368..30821072-chr22:30821188..30822984,2	MCF-7	breast:
19	chr22:30767828..30769825-chr22:30819204..30821511,2	MCF-7	breast:
20	chr22:30818782..30821257-chr22:30824236..30826444,3	MCF-7	breast:
21	chr22:30805177..30806953-chr22:30818450..30820693,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272689	TF binding region
RNF215	TF binding region
MTFP1	TF binding region
ENSG00000239282	Chromatin interaction
ENSG00000222915	Chromatin interaction
ENSG00000099992	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000273350	Chromatin interaction
ENSG00000187860	Chromatin interaction
ENSG00000203606	Chromatin interaction
ENSG00000249590	Chromatin interaction
ENSG00000184792	Chromatin interaction
ENSG00000100003	Chromatin interaction
ENSG00000099985	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000242114	Chromatin interaction
ENSG00000272689	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2108093	0.80[CHD][hapmap]
rs2299830	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4339043	0.80[CHD][hapmap]
rs4820012	0.86[ASN][1000 genomes]
rs4820844	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap]
rs5749082	0.92[CEU][hapmap]
rs5753080	0.80[CHD][hapmap]
rs5753134	0.86[ASN][1000 genomes]
rs737723	0.84[MEX][hapmap]
rs737950	0.80[CHD][hapmap]
rs740219	0.80[CHD][hapmap]
rs929454	0.80[CHD][hapmap]
rs9608904	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1046199	ZNF302	trans	parietal	SCAN
rs1046199	SF3A1	cis	multi-tissue	Pritchard
rs1046199	RFPL2	cis	parietal	SCAN
rs1046199	C22orf42	cis	parietal	SCAN
rs1046199	OR4N5	trans	cerebellum	SCAN
rs1046199	ZNRF3	cis	parietal	SCAN
rs1046199	PAIP2B	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30818000-30821600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
2	chr22:30818400-30820600	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr22:30818400-30820800	Active TSS	K562	blood
4	chr22:30818400-30821600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr22:30818600-30820600	Active TSS	Right Atrium	heart
6	chr22:30818600-30821800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr22:30818600-30821800	Flanking Active TSS	NHEK	skin
8	chr22:30818600-30822400	Active TSS	Fetal Kidney	kidney
9	chr22:30818600-30822600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr22:30818600-30822600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr22:30818600-30822800	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr22:30818600-30823000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr22:30818800-30820600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr22:30818800-30820600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr22:30818800-30820600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr22:30818800-30820600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr22:30818800-30820600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr22:30818800-30820600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr22:30818800-30820600	Active TSS	Ovary	ovary
20	chr22:30818800-30820600	Active TSS	A549	lung
21	chr22:30818800-30822600	Active TSS	Psoas Muscle	Psoas
22	chr22:30819000-30820600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr22:30819000-30820600	Active TSS	Aorta	Aorta
24	chr22:30819000-30820600	Active TSS	Esophagus	oesophagus
25	chr22:30819000-30820600	Flanking Active TSS	Placenta	Placenta
26	chr22:30819000-30820600	Active TSS	Left Ventricle	heart
27	chr22:30819000-30820800	Active TSS	H1 Cell Line	embryonic stem cell
28	chr22:30819000-30820800	Active TSS	H9 Cell Line	embryonic stem cell
29	chr22:30819000-30820800	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr22:30819000-30820800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr22:30819000-30820800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr22:30819000-30820800	Active TSS	Fetal Brain Female	brain
33	chr22:30819000-30820800	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr22:30819000-30821800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr22:30819000-30822200	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr22:30819000-30822600	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr22:30819000-30822600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr22:30819000-30822800	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr22:30819200-30820600	Active TSS	Brain Angular Gyrus	brain
40	chr22:30819200-30820600	Active TSS	Gastric	stomach
41	chr22:30819200-30820600	Active TSS	Right Ventricle	heart
42	chr22:30819200-30820800	Active TSS	Small Intestine	intestine
43	chr22:30819200-30821000	Flanking Active TSS	HMEC	breast
44	chr22:30819200-30822600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr22:30819200-30823000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr22:30819400-30820600	Active TSS	Brain Cingulate Gyrus	brain
47	chr22:30819400-30820600	Active TSS	Brain Substantia Nigra	brain
48	chr22:30819400-30820600	Active TSS	Fetal Intestine Large	intestine
49	chr22:30819400-30820600	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr22:30819400-30820800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links