Variant report

Variant	rs12306942
Chromosome Location	chr12:49915092-49915093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49912988..49915445-chr12:49916293..49919057,4	K562	blood:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11169055	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169071	1.00[EUR][1000 genomes]
rs11830622	1.00[AMR][1000 genomes]
rs11831670	1.00[EUR][1000 genomes]
rs11834883	1.00[AMR][1000 genomes]
rs11835085	1.00[EUR][1000 genomes]
rs11836969	1.00[AMR][1000 genomes]
rs12296998	1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12298123	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12298506	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299477	1.00[EUR][1000 genomes]
rs12299743	1.00[EUR][1000 genomes]
rs12300085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12309399	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12310046	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12311319	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12311910	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12313583	1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12314348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12315746	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12315941	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12318913	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12319527	1.00[EUR][1000 genomes]
rs12320104	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12320434	1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12320612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12321717	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13377828	1.00[AMR][1000 genomes]
rs28420769	1.00[EUR][1000 genomes]
rs57970210	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58867453	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59250711	1.00[AMR][1000 genomes]
rs59570650	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59576871	1.00[EUR][1000 genomes]
rs60254449	1.00[AMR][1000 genomes]
rs60507124	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60658484	1.00[AMR][1000 genomes]
rs61227990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7960185	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv518746	chr12:49870964-49924637	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49823000-49915800	Weak transcription	Primary B cells from cord blood	blood
2	chr12:49869600-49918400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:49873000-49918800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:49873200-49918600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:49876800-49916200	Weak transcription	Psoas Muscle	Psoas
6	chr12:49878600-49918600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:49880400-49916000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:49882200-49918800	Weak transcription	Colonic Mucosa	Colon
9	chr12:49882400-49918400	Weak transcription	Lung	lung
10	chr12:49882600-49916400	Weak transcription	Aorta	Aorta
11	chr12:49884200-49918400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:49884200-49918600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:49884600-49916400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:49886000-49918400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:49886400-49918200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:49888800-49927800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:49890800-49918600	Weak transcription	Brain Anterior Caudate	brain
18	chr12:49890800-49918600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:49891000-49916600	Weak transcription	Ovary	ovary
20	chr12:49893600-49915200	Weak transcription	Placenta	Placenta
21	chr12:49894000-49916600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:49894000-49919600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:49894400-49915400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr12:49896000-49916800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:49896400-49916600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:49896800-49916400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:49896800-49916400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:49896800-49916600	Weak transcription	Fetal Thymus	thymus
29	chr12:49898200-49916400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr12:49898200-49918400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:49900000-49916400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:49900600-49916400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:49900600-49916600	Weak transcription	Left Ventricle	heart
34	chr12:49905000-49918600	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:49905200-49915800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr12:49905200-49927000	Weak transcription	Fetal Heart	heart
37	chr12:49905400-49918400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:49905600-49919000	Weak transcription	HepG2	liver
39	chr12:49907200-49918400	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:49909600-49916400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:49909600-49918800	Weak transcription	HMEC	breast
42	chr12:49909600-49925600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:49909800-49915400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:49909800-49918600	Weak transcription	Liver	Liver
45	chr12:49910600-49921600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:49911000-49923000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:49911200-49922000	Strong transcription	Fetal Intestine Large	intestine
48	chr12:49911400-49916400	Weak transcription	Fetal Lung	lung
49	chr12:49911400-49917200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:49911400-49918400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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