Variant report

Variant	rs2291612
Chromosome Location	chr12:50410533-50410534
allele	A/G
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	MXI1	chr12:50410164-50411417	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50395877..50398292-chr12:50410498..50412765,2	K562	blood:

Variant related genes	Relation type
RACGAP1	TF binding region
ENSG00000161800	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10161020	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10161120	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875990	0.90[GIH][hapmap]
rs10875992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs10875993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169232	0.86[EUR][1000 genomes]
rs11169234	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11169256	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169259	0.98[EUR][1000 genomes]
rs11169260	0.98[EUR][1000 genomes]
rs11835014	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11836389	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298110	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12311010	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12317586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17124264	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292720	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2307082	0.86[JPT][hapmap]
rs378943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs4297542	1.00[EUR][1000 genomes]
rs55634523	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55652312	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55802497	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55936104	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55990533	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56099252	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56159935	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56232366	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56259551	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57014171	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57045365	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60000653	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60042968	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60456498	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60905953	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611434	0.94[EUR][1000 genomes]
rs615382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs629754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs661823	0.83[EUR][1000 genomes]
rs694851	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[EUR][1000 genomes]
rs7131715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306035	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7308994	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309480	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7309940	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7309966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73119648	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73119651	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73119660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73119664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73119671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73119681	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73119688	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73119690	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7961683	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7972522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7979958	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9325146	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9669608	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong 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	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
7	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	28 gene(s)	inside rSNPs	diseases
9	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50369600-50418200	Weak transcription	Colonic Mucosa	Colon
2	chr12:50378600-50412800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:50380400-50410600	Weak transcription	Aorta	Aorta
4	chr12:50382000-50414800	Weak transcription	Psoas Muscle	Psoas
5	chr12:50383000-50418000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:50387600-50411800	Weak transcription	Lung	lung
7	chr12:50387800-50411600	Weak transcription	Esophagus	oesophagus
8	chr12:50388200-50418000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:50391000-50418000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr12:50392800-50418200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:50393400-50411000	Weak transcription	Fetal Brain Female	brain
12	chr12:50393600-50411000	Weak transcription	Liver	Liver
13	chr12:50395400-50412200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:50397600-50412000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:50399200-50418200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:50399400-50412800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:50399800-50410800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:50399800-50417400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:50400400-50411800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr12:50400400-50418200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:50400600-50418200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:50400800-50410800	Weak transcription	HUVEC	blood vessel
23	chr12:50401200-50418200	Weak transcription	Primary B cells from cord blood	blood
24	chr12:50401400-50410600	Weak transcription	Fetal Kidney	kidney
25	chr12:50401400-50410600	Weak transcription	NHLF	lung
26	chr12:50401400-50412800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:50403000-50418600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:50403200-50413000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:50404400-50410800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:50405400-50412000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:50406400-50411200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:50406600-50410800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:50407000-50410600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:50407000-50411800	Strong transcription	Fetal Thymus	thymus
35	chr12:50407000-50412800	Strong transcription	Hela-S3	cervix
36	chr12:50407200-50410600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:50407200-50411200	Strong transcription	NHEK	skin
38	chr12:50407200-50411400	Strong transcription	HMEC	breast
39	chr12:50407200-50412800	Strong transcription	Dnd41	blood
40	chr12:50407400-50410600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:50407400-50410600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:50407600-50411000	Weak transcription	HSMM	muscle
43	chr12:50407800-50410600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr12:50407800-50415000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:50407800-50418000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:50408200-50411200	Strong transcription	Thymus	Thymus
47	chr12:50408400-50410600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:50408400-50410600	Weak transcription	Osteobl	bone
49	chr12:50408400-50415000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:50408400-50418000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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