Variant report

Variant	rs12296246
Chromosome Location	chr12:32394562-32394563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12297959	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298558	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12307772	0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs12307792	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12308522	0.85[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309702	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12310014	0.85[CEU][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310030	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12312114	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12317181	0.96[YRI][hapmap];0.99[AFR][1000 genomes]
rs12317202	0.85[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319221	0.85[AFR][1000 genomes]
rs16916339	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919488	0.83[GIH][hapmap]
rs16919521	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs16919525	1.00[CEU][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16919527	0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2594009	0.84[YRI][hapmap]
rs2594010	0.82[YRI][hapmap]
rs2650142	0.88[YRI][hapmap]
rs2650144	0.84[YRI][hapmap]
rs2650145	0.84[YRI][hapmap]
rs28427470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55766406	0.88[EUR][1000 genomes]
rs56007954	0.91[EUR][1000 genomes]
rs56075891	0.86[EUR][1000 genomes]
rs56254678	0.86[EUR][1000 genomes]
rs58801621	0.82[EUR][1000 genomes]
rs59032949	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6488039	1.00[CEU][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7134330	0.86[EUR][1000 genomes]
rs7136736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7136837	1.00[CEU][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7136969	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7137031	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7137148	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73310707	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73310709	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73310720	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73310734	0.87[AFR][1000 genomes]
rs73310736	0.87[AFR][1000 genomes]
rs73310737	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73310739	0.82[AFR][1000 genomes]
rs7956048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7957547	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959439	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962134	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7962447	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7962525	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7970958	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971625	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7974961	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7977350	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers 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	41 gene(s)	inside rSNPs	diseases
2	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv832366	chr12:32328559-32511360	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv541454	chr12:32371080-32401245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32370200-32407800	Weak transcription	Hela-S3	cervix
2	chr12:32371200-32406800	Weak transcription	Primary T cells from cord blood	blood
3	chr12:32380000-32401000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:32390400-32397200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:32390600-32399600	Weak transcription	Dnd41	blood
6	chr12:32390600-32400600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:32390600-32402400	Weak transcription	HSMMtube	muscle
8	chr12:32390800-32401600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:32390800-32405400	Weak transcription	Ovary	ovary
10	chr12:32390800-32410600	Weak transcription	Primary B cells from cord blood	blood
11	chr12:32391000-32401000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:32391000-32401400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:32391200-32401000	Weak transcription	Fetal Intestine Small	intestine
14	chr12:32391200-32401600	Weak transcription	Aorta	Aorta
15	chr12:32391200-32405200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:32391200-32408000	Weak transcription	Fetal Brain Female	brain
17	chr12:32391200-32409200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:32391400-32401000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:32391600-32401200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:32391600-32402600	Weak transcription	HSMM	muscle
21	chr12:32391600-32408000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:32393600-32394600	Enhancers	HUVEC	blood vessel
23	chr12:32393600-32396600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:32393600-32398200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:32393600-32399400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:32393600-32410400	Weak transcription	NHLF	lung
27	chr12:32393600-32423800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:32393800-32394600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:32394000-32398400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:32394000-32401600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:32394000-32401800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:32394000-32424200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:32394200-32398400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:32394200-32401200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:32394200-32405600	Weak transcription	A549	lung
36	chr12:32394400-32394600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:32394400-32423800	Weak transcription	NH-A	brain

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