Variant report

Variant	rs1870197
Chromosome Location	chr12:822664-822665
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:822480..827590-chr12:828895..833906,6	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10161428	0.95[ASN][1000 genomes]
rs10849496	0.89[ASN][1000 genomes]
rs10849497	0.91[ASN][1000 genomes]
rs10849514	0.95[ASN][1000 genomes]
rs10849515	0.98[ASN][1000 genomes]
rs10849528	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11064327	0.93[ASN][1000 genomes]
rs11064364	0.93[ASN][1000 genomes]
rs11064365	0.93[ASN][1000 genomes]
rs11064366	0.93[ASN][1000 genomes]
rs11064367	0.93[ASN][1000 genomes]
rs11064378	0.86[ASN][1000 genomes]
rs11064395	0.98[ASN][1000 genomes]
rs11064496	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12366513	0.93[ASN][1000 genomes]
rs12371774	0.95[ASN][1000 genomes]
rs1870203	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs35758984	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4417362	0.95[ASN][1000 genomes]
rs4468405	0.93[ASN][1000 genomes]
rs4980964	0.93[ASN][1000 genomes]
rs7132931	0.93[ASN][1000 genomes]
rs7488059	0.93[ASN][1000 genomes]
rs7957753	0.95[ASN][1000 genomes]
rs7958125	0.95[ASN][1000 genomes]
rs7959183	0.95[ASN][1000 genomes]
rs7962483	0.93[ASN][1000 genomes]
rs7965115	0.91[ASN][1000 genomes]
rs7967078	0.95[ASN][1000 genomes]
rs9645766	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1870197	EFCAB4B	cis	cerebellum	SCAN
rs1870197	ITFG2	cis	parietal	SCAN
rs1870197	FOXM1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:792000-825600	Weak transcription	Right Atrium	heart
2	chr12:809800-822800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:810000-825400	Weak transcription	Primary T cells from cord blood	blood
4	chr12:812800-823000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:813200-828200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:814200-828000	Weak transcription	Primary B cells from cord blood	blood
7	chr12:819000-822800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:819200-822800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:819200-822800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:821200-822800	Enhancers	Primary hematopoietic stem cells	blood
11	chr12:821200-822800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:821200-823000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:821200-823000	Enhancers	Brain Cingulate Gyrus	brain
14	chr12:821200-823200	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr12:821200-823200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr12:821200-823200	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr12:821200-823200	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr12:821200-823200	Enhancers	K562	blood
19	chr12:821200-823400	Enhancers	Brain Hippocampus Middle	brain
20	chr12:821400-823200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr12:821400-823200	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr12:821400-823200	Enhancers	Brain Substantia Nigra	brain
23	chr12:821400-823200	Enhancers	Fetal Muscle Leg	muscle
24	chr12:821400-823200	Enhancers	Fetal Thymus	thymus
25	chr12:821400-823400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr12:821600-823000	Enhancers	HepG2	liver
27	chr12:821800-822800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:821800-822800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:821800-828000	Weak transcription	Thymus	Thymus
30	chr12:822000-822800	Enhancers	Fetal Heart	heart
31	chr12:822000-823200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:822000-823200	Enhancers	Brain Angular Gyrus	brain
33	chr12:822000-825800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:822000-827200	Weak transcription	GM12878-XiMat	blood
35	chr12:822000-828000	Weak transcription	HSMM	muscle
36	chr12:822000-835600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:822200-823000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:822400-823000	Enhancers	Brain Anterior Caudate	brain
39	chr12:822400-823000	Enhancers	HSMMtube	muscle
40	chr12:822600-823000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr12:822600-823000	Active TSS	Right Ventricle	heart
42	chr12:822600-823200	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr12:822600-823200	Enhancers	Skeletal Muscle Female	skeletal muscle

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