Variant report

Variant	rs2228224
Chromosome Location	chr12:57865321-57865322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr12:57865084-57865338	HepG2	liver:	n/a	chr12:57865163-57865178
2	POLR2A	chr12:57862773-57865886	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:57865302-57865974	GM12892	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57861880..57866210-chr12:57903608..57907475,3	K562	blood:
2	chr12:57856210..57858089-chr12:57864430..57867371,4	K562	blood:
3	chr12:57854179..57856713-chr12:57863394..57866070,2	MCF-7	breast:
4	chr12:57864997..57867695-chr12:57880330..57882792,2	K562	blood:
5	chr12:57858695..57861784-chr12:57862109..57867144,5	K562	blood:
6	chr12:57863342..57866223-chr12:57872034..57874836,2	MCF-7	breast:
7	chr12:57864629..57868923-chr12:57913251..57916366,4	K562	blood:
8	chr12:57847573..57850559-chr12:57865092..57866991,2	K562	blood:
9	chr12:57863008..57865663-chr12:57869026..57873424,5	K562	blood:
10	chr12:57864949..57866728-chr12:57912864..57915188,2	MCF-7	breast:
11	chr12:57864629..57868317-chr12:57913861..57916135,3	K562	blood:
12	chr12:57850914..57853325-chr12:57864861..57866988,3	K562	blood:

No data

Variant related genes	Relation type
MARS	TF binding region
ENSG00000208028	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000252865	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000166987	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10783827	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs10783828	0.80[CEU][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10876986	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876987	0.80[ASN][1000 genomes]
rs11544238	0.91[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2228225	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2228226	0.80[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2277315	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2277316	0.80[CEU][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2277317	0.80[CEU][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2277318	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2292657	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3782125	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3782126	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817474	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817475	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3825077	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760148	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760255	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4760259	0.80[CEU][hapmap]
rs7309467	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription 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 miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers 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 miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv8974	chr12:57852779-57865881	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	n/a
14	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
15	nsv559035	chr12:57860972-57870648	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2228224	ATF7	cis	cerebellum	SCAN
rs2228224	ITGA5	cis	cerebellum	SCAN
rs2228224	ITGB7	cis	cerebellum	SCAN
rs2228224	OR6C4	cis	parietal	SCAN
rs2228224	RDH5	cis	cerebellum	SCAN
rs2228224	FAM119B	cis	cerebellum	SCAN
rs2228224	KIAA0748	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57856600-57865800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:57856800-57865600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr12:57856800-57866200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:57857000-57865800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:57857000-57868400	Weak transcription	Dnd41	blood
6	chr12:57857000-57869400	Weak transcription	Ovary	ovary
7	chr12:57857200-57866200	Strong transcription	Fetal Stomach	stomach
8	chr12:57857400-57865800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:57857800-57865400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:57859400-57865800	Strong transcription	Fetal Muscle Leg	muscle
11	chr12:57859600-57870800	Weak transcription	A549	lung
12	chr12:57860600-57866200	Strong transcription	Primary T cells from cord blood	blood
13	chr12:57861000-57868000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:57861200-57868600	Strong transcription	Fetal Thymus	thymus
15	chr12:57861400-57868400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:57861400-57868600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:57861800-57865600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:57861800-57869600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:57862600-57868200	Strong transcription	Thymus	Thymus
20	chr12:57862800-57868400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:57862800-57869400	Genic enhancers	Primary monocytes fromperipheralblood	blood
22	chr12:57862800-57870400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
23	chr12:57863000-57865400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr12:57863000-57865600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr12:57863000-57865800	Bivalent Enhancer	HepG2	liver
26	chr12:57863000-57866000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:57863000-57866000	Genic enhancers	Fetal Intestine Small	intestine
28	chr12:57863000-57866400	Enhancers	Fetal Intestine Large	intestine
29	chr12:57863000-57869000	Genic enhancers	Monocytes-CD14+_RO01746	blood
30	chr12:57863200-57869400	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr12:57863400-57868800	Weak transcription	Lung	lung
32	chr12:57863400-57869000	Weak transcription	Pancreas	Pancrea
33	chr12:57863600-57868000	Weak transcription	K562	blood
34	chr12:57864000-57867800	Genic enhancers	Primary B cells from cord blood	blood
35	chr12:57864000-57869400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:57864200-57865800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:57864200-57868000	Strong transcription	Primary hematopoietic stem cells	blood
38	chr12:57864200-57868600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr12:57864200-57869200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr12:57864400-57865400	Enhancers	Colonic Mucosa	Colon
41	chr12:57864400-57865400	Enhancers	Stomach Mucosa	stomach
42	chr12:57864400-57865400	Strong transcription	Spleen	Spleen
43	chr12:57864400-57865800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr12:57864600-57865400	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr12:57864600-57865600	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr12:57864600-57868600	Weak transcription	Liver	Liver
47	chr12:57864600-57869000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr12:57864600-57869200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr12:57864800-57865600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr12:57864800-57865600	Enhancers	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links