Variant report

Variant	rs12312965
Chromosome Location	chr12:105592526-105592527
allele	G/T
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	POLR2A	chr12:105591786-105592957	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:105592271-105593074	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:105590936-105593428	A549	lung:	n/a	n/a
4	POLR2A	chr12:105592316-105592745	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr12:105590989-105593042	HUVEC	blood vessel:	n/a	n/a
6	ZNF263	chr12:105592373-105592776	HEK293-T-REx	kidney:	n/a	n/a
7	POLR2A	chr12:105592220-105592872	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr12:105590584-105592945	GM12891	blood:	n/a	n/a
9	POLR2A	chr12:105590596-105593424	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:105590825-105593473	K562	blood:	n/a	n/a
11	POLR2A	chr12:105592003-105593538	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr12:105592111-105592737	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr12:105592525-105593121	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:105591334-105593170	HUVEC	blood vessel:	n/a	n/a
15	MAX	chr12:105592492-105592989	NB4	blood:	n/a	chr12:105592791-105592801
16	POLR2A	chr12:105591170-105593542	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105592344..105594615-chr12:105595221..105597389,2	MCF-7	breast:
2	chr12:105501608..105503179-chr12:105592060..105594445,2	K562	blood:

Variant related genes	Relation type
APPL2	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10083185	0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11112381	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11112389	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11112410	0.88[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11559871	0.85[EUR][1000 genomes]
rs11829598	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1196852	0.82[YRI][hapmap]
rs12299366	0.92[EUR][1000 genomes]
rs12299391	0.92[EUR][1000 genomes]
rs12301914	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12304384	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12305766	0.85[EUR][1000 genomes]
rs12307372	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12311156	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12317637	0.87[EUR][1000 genomes]
rs12317804	0.92[EUR][1000 genomes]
rs12321199	0.92[EUR][1000 genomes]
rs12321518	0.89[EUR][1000 genomes]
rs12321534	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12424191	0.89[EUR][1000 genomes]
rs12424709	0.89[EUR][1000 genomes]
rs12425803	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3910856	0.87[CEU][hapmap]
rs56284118	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56862143	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59320697	0.89[EUR][1000 genomes]
rs59593474	0.92[EUR][1000 genomes]
rs60835294	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60999193	0.92[EUR][1000 genomes]
rs7132816	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7133728	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7136453	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7138574	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7300130	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7302842	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7305406	0.89[EUR][1000 genomes]
rs7313309	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7315964	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73179990	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73179996	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73179998	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73180001	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181822	0.89[EUR][1000 genomes]
rs73181857	0.85[EUR][1000 genomes]
rs7964184	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7971630	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7975787	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7978034	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:105561400-105598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:105571400-105617800	Weak transcription	K562	blood
5	chr12:105576000-105593200	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr12:105576000-105595600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:105576400-105606000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:105577000-105607200	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:105577400-105592800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:105577400-105593600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:105577800-105592600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:105577800-105593400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:105577800-105594200	Strong transcription	Fetal Intestine Large	intestine
15	chr12:105577800-105594400	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:105577800-105595200	Strong transcription	Left Ventricle	heart
17	chr12:105577800-105598600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:105577800-105598800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr12:105577800-105599400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:105577800-105602600	Strong transcription	Fetal Thymus	thymus
21	chr12:105577800-105603600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:105577800-105605400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:105577800-105605600	Strong transcription	Primary B cells from cord blood	blood
24	chr12:105577800-105607400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr12:105578000-105593000	Strong transcription	Osteobl	bone
26	chr12:105578000-105593400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:105578000-105593400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:105578000-105599200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr12:105578000-105607400	Strong transcription	Fetal Brain Female	brain
30	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:105578200-105593600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr12:105578400-105593400	Strong transcription	NHLF	lung
34	chr12:105578400-105602400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:105578800-105592800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:105579000-105593000	Strong transcription	NHEK	skin
37	chr12:105579000-105598600	Strong transcription	HSMM	muscle
38	chr12:105579000-105605200	Strong transcription	Fetal Muscle Leg	muscle
39	chr12:105579000-105612400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr12:105579200-105593400	Strong transcription	Placenta	Placenta
41	chr12:105579400-105593000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:105579400-105595000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:105579800-105593000	Strong transcription	Fetal Lung	lung
44	chr12:105579800-105596000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:105580200-105613200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:105581200-105602600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:105581200-105605400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr12:105581400-105595000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:105581800-105602600	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:105581800-105605200	Strong transcription	Brain Germinal Matrix	brain

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