Variant report

Variant	rs12316220
Chromosome Location	chr12:51406951-51406952
allele	C/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	RCOR1	chr12:51406654-51407034	K562	blood:	n/a	n/a
2	GATA3	chr12:51406429-51407122	SK-N-SH	brain:	n/a	chr12:51406814-51406821
3	GATA3	chr12:51406505-51407147	SK-N-SH	brain:	n/a	chr12:51406814-51406821
4	GATA3	chr12:51406669-51407038	T-47D	breast:	n/a	chr12:51406814-51406821
5	EP300	chr12:51406706-51407017	SK-N-SH_RA	brain:	n/a	chr12:51406774-51406788
6	EP300	chr12:51406619-51406971	SK-N-SH_RA	brain:	n/a	chr12:51406774-51406788
7	TEAD4	chr12:51406622-51407057	K562	blood:	n/a	n/a
8	PBX3	chr12:51406638-51407061	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr12:51406648-51407001	T-47D	breast:	n/a	chr12:51406814-51406821
10	SPI1	chr12:51406692-51407031	HL-60	blood:	n/a	chr12:51406887-51406900 chr12:51406886-51406899 chr12:51406889-51406898

No.	Distal block	Cell Line	Cell type
1	chr12:51405834..51407705-chr12:51409196..51411163,3	K562	blood:
2	chr12:51397497..51399942-chr12:51404608..51407015,3	MCF-7	breast:
3	chr12:51157683..51159798-chr12:51405816..51407695,2	MCF-7	breast:
4	chr12:51404460..51409575-chr12:51416331..51420356,8	MCF-7	breast:
5	chr12:51397539..51404278-chr12:51405080..51409503,9	MCF-7	breast:
6	chr12:51156953..51158671-chr12:51406761..51408845,2	K562	blood:

Variant related genes	Relation type
SLC11A2	TF binding region
ENSG00000110911	Chromatin interaction
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1096028	1.00[EUR][1000 genomes]
rs1096029	1.00[EUR][1000 genomes]
rs11169705	1.00[EUR][1000 genomes]
rs11169713	1.00[EUR][1000 genomes]
rs11542510	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs11832566	0.89[LWK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs11833478	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12301714	1.00[YRI][hapmap]
rs12307173	1.00[EUR][1000 genomes]
rs12321533	1.00[YRI][hapmap]
rs1595597	1.00[EUR][1000 genomes]
rs1642998	1.00[EUR][1000 genomes]
rs2554869	1.00[EUR][1000 genomes]
rs7134808	0.81[YRI][hapmap]
rs7342309	0.81[YRI][hapmap]
rs7973984	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7978782	1.00[EUR][1000 genomes]
rs829116	1.00[EUR][1000 genomes]
rs829117	1.00[EUR][1000 genomes]
rs829118	1.00[EUR][1000 genomes]
rs829119	1.00[EUR][1000 genomes]
rs829121	1.00[EUR][1000 genomes]
rs829136	1.00[EUR][1000 genomes]
rs829137	1.00[EUR][1000 genomes]
rs829138	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51386000-51414200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:51399200-51418000	Weak transcription	Gastric	stomach
3	chr12:51399400-51408200	Weak transcription	NHDF-Ad	bronchial
4	chr12:51399800-51414600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:51399800-51415600	Weak transcription	Right Ventricle	heart
6	chr12:51400000-51407200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:51400000-51407400	Weak transcription	HMEC	breast
8	chr12:51401000-51410800	Weak transcription	HepG2	liver
9	chr12:51401400-51417800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:51401600-51410000	Weak transcription	Pancreas	Pancrea
11	chr12:51402000-51418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:51402000-51418000	Weak transcription	Fetal Stomach	stomach
13	chr12:51402400-51407200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr12:51402400-51407200	Weak transcription	Lung	lung
15	chr12:51402400-51408600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:51402400-51415600	Weak transcription	GM12878-XiMat	blood
17	chr12:51402400-51417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:51402400-51417600	Weak transcription	Left Ventricle	heart
19	chr12:51402400-51418000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:51403000-51418000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:51403200-51407600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:51403400-51407600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr12:51403400-51415600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:51403400-51417600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:51403600-51407000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:51403600-51407400	Enhancers	Brain Hippocampus Middle	brain
27	chr12:51403600-51407600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr12:51403600-51410200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:51403600-51412000	Weak transcription	Fetal Intestine Small	intestine
30	chr12:51403600-51414200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:51403600-51414400	Weak transcription	Hela-S3	cervix
32	chr12:51403600-51414600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:51403600-51417400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:51403600-51417600	Weak transcription	HSMM	muscle
35	chr12:51403800-51411200	Weak transcription	Fetal Intestine Large	intestine
36	chr12:51403800-51412800	Weak transcription	Primary T cells from cord blood	blood
37	chr12:51403800-51412800	Weak transcription	Dnd41	blood
38	chr12:51403800-51417000	Weak transcription	Brain Germinal Matrix	brain
39	chr12:51404000-51407200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr12:51404000-51411400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr12:51404200-51411200	Weak transcription	Fetal Thymus	thymus
42	chr12:51404200-51411200	Weak transcription	Ovary	ovary
43	chr12:51404200-51411200	Weak transcription	Thymus	Thymus
44	chr12:51404200-51414600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:51404800-51417800	Weak transcription	Fetal Brain Female	brain
46	chr12:51405600-51407000	Enhancers	Brain Cingulate Gyrus	brain
47	chr12:51405600-51407200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr12:51405600-51407400	Enhancers	HSMMtube	muscle
49	chr12:51405600-51407600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:51405800-51407000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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