Variant report

Variant	rs9645766
Chromosome Location	chr12:825782-825783
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:825603..828799-chr12:857363..861650,3	K562	blood:
2	chr12:824399..827215-chr12:865443..868265,2	K562	blood:
3	chr12:818532..821331-chr12:822970..825882,2	K562	blood:
4	chr12:824394..827351-chr12:860045..863016,2	K562	blood:
5	chr12:822480..827590-chr12:828895..833906,6	K562	blood:

Variant related genes	Relation type
ENSG00000060237	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10161428	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10849496	0.89[ASN][1000 genomes]
rs10849497	0.91[ASN][1000 genomes]
rs10849514	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10849515	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10849528	0.89[ASN][1000 genomes]
rs11064327	0.93[ASN][1000 genomes]
rs11064364	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11064365	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11064366	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11064367	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11064378	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11064395	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11064496	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12366513	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12371774	0.91[ASN][1000 genomes]
rs1870197	0.95[ASN][1000 genomes]
rs4417362	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4468405	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4980964	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7132931	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7488059	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7957753	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7958125	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7959183	0.95[ASN][1000 genomes]
rs7962483	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7965115	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7967078	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1053519	chr12:321619-828175	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	esv2759875	chr12:335010-990544	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
9	nsv1045638	chr12:349031-893536	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
10	nsv541325	chr12:349031-893536	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
11	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
12	esv2758290	chr12:457433-990544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv898567	chr12:547683-863517	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
14	nsv898568	chr12:547683-969800	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
15	nsv491937	chr12:574727-835424	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	nsv1049625	chr12:595867-840090	Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv541331	chr12:595867-840090	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv556887	chr12:632240-867504	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
19	nsv556890	chr12:662448-1100555	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
20	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
21	nsv1051590	chr12:722215-974773	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
22	nsv541338	chr12:722215-974773	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
23	nsv468956	chr12:737230-982321	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
24	nsv556893	chr12:737230-982321	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
25	esv2757485	chr12:786238-964551	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
26	nsv1043718	chr12:786563-855811	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	nsv541339	chr12:786563-855811	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
28	nsv1046707	chr12:792110-910520	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
29	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9645766	ITFG2	cis	parietal	SCAN
rs9645766	FKBP4	cis	parietal	SCAN
rs9645766	MAP6D1	trans	cerebellum	SCAN
rs9645766	FOXM1	cis	cerebellum	SCAN
rs9645766	EFCAB4B	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:813200-828200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:814200-828000	Weak transcription	Primary B cells from cord blood	blood
3	chr12:821800-828000	Weak transcription	Thymus	Thymus
4	chr12:822000-825800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:822000-827200	Weak transcription	GM12878-XiMat	blood
6	chr12:822000-828000	Weak transcription	HSMM	muscle
7	chr12:822000-835600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:823000-828000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:823000-828000	Weak transcription	Brain Anterior Caudate	brain
10	chr12:823000-828000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:823000-828200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:823000-828200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:823200-827400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr12:823200-828000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:823200-828000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:823200-828000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:823200-828000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:823200-828000	Weak transcription	Brain Angular Gyrus	brain
19	chr12:823200-828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:823200-828000	Weak transcription	Brain Substantia Nigra	brain
21	chr12:823200-828200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:823200-828200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:823200-828400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:823200-828400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:823200-831400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:823400-825800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:823400-826400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr12:823400-826400	Weak transcription	Left Ventricle	heart
29	chr12:823400-828000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:823400-828000	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:823600-828200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:824000-832000	Enhancers	Fetal Muscle Leg	muscle
33	chr12:825000-826200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:825000-826800	Enhancers	Fetal Thymus	thymus
35	chr12:825400-825800	Active TSS	Right Ventricle	heart
36	chr12:825400-826000	Flanking Active TSS	Fetal Heart	heart
37	chr12:825400-826200	Enhancers	Primary T cells from cord blood	blood
38	chr12:825400-826200	Enhancers	Primary hematopoietic stem cells	blood
39	chr12:825400-826200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr12:825400-826200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:825600-825800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr12:825600-826000	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr12:825600-826000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr12:825600-826000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr12:825600-826000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr12:825600-826000	Active TSS	Right Atrium	heart
47	chr12:825600-826200	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr12:825600-826200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:825600-826200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr12:825600-826200	Enhancers	HSMMtube	muscle

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