Variant report

Variant	rs10850664
Chromosome Location	chr12:116996826-116996827
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	POU2F2	chr12:116996623-116997989	GM12891	blood:	n/a	n/a
2	NR2F2	chr12:116996765-116997915	K562	blood:	n/a	chr12:116997277-116997292
3	TEAD4	chr12:116996259-116997976	K562	blood:	n/a	n/a
4	ZEB1	chr12:116996698-116997097	GM12878	blood:	n/a	n/a
5	ELF1	chr12:116996653-116997296	GM12878	blood:	n/a	n/a
6	TEAD4	chr12:116996446-116997997	K562	blood:	n/a	n/a
7	RELA	chr12:116996344-116997988	GM12878	blood:	n/a	n/a
8	MEF2C	chr12:116996615-116998014	GM12878	blood:	n/a	chr12:116996877-116996894
9	MAX	chr12:116996231-116997968	NB4	blood:	n/a	chr12:116997426-116997436
10	PAX5	chr12:116996645-116997966	GM12878	blood:	n/a	chr12:116997680-116997699 chr12:116997629-116997638 chr12:116997085-116997112
11	NFYB	chr12:116996824-116997857	GM12878	blood:	n/a	n/a
12	MAX	chr12:116996715-116997928	K562	blood:	n/a	chr12:116997426-116997436
13	POLR2A	chr12:116996734-116997007	GM12878	blood:	n/a	n/a
14	TBP	chr12:116996713-116997907	GM12878	blood:	n/a	n/a
15	BATF	chr12:116996694-116997973	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:116996246-116997914	K562	blood:	n/a	n/a
17	MXI1	chr12:116996255-116996872	K562	blood:	n/a	n/a
18	MEF2A	chr12:116996754-116998070	GM12878	blood:	n/a	chr12:116996877-116996894
19	EP300	chr12:116996817-116997938	GM12878	blood:	n/a	chr12:116997517-116997527 chr12:116997875-116997889 chr12:116997832-116997846
20	POLR2A	chr12:116996222-116997943	Raji	blood:	n/a	n/a
21	RELA	chr12:116996328-116997999	GM19099	blood:	n/a	n/a
22	TCF12	chr12:116996704-116997984	GM12878	blood:	n/a	chr12:116997517-116997526
23	RELA	chr12:116996357-116997990	GM18505	blood:	n/a	n/a
24	WRNIP1	chr12:116996783-116997951	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:116996178-116998040	GM12878	blood:	n/a	n/a
26	BCL3	chr12:116996682-116997960	GM12878	blood:	n/a	chr12:116997629-116997638
27	PAX5	chr12:116996809-116997900	GM12878	blood:	n/a	chr12:116997680-116997699 chr12:116997629-116997638 chr12:116997085-116997112
28	POLR2A	chr12:116996226-116997897	GM12891	blood:	n/a	n/a
29	POLR2A	chr12:116996062-116997895	GM12892	blood:	n/a	n/a
30	EP300	chr12:116996214-116997965	K562	blood:	n/a	chr12:116997517-116997527 chr12:116997875-116997889 chr12:116997832-116997846
31	CHD2	chr12:116996785-116997969	GM12878	blood:	n/a	n/a
32	TBL1XR1	chr12:116996637-116998014	GM12878	blood:	n/a	n/a
33	SRF	chr12:116996735-116996990	GM12878	blood:	n/a	chr12:116996877-116996895 chr12:116996881-116996895
34	TAL1	chr12:116996215-116997918	K562	blood:	n/a	n/a
35	SPI1	chr12:116996735-116997953	GM12878	blood:	n/a	chr12:116997629-116997638
36	POLR2A	chr12:116996168-116997858	K562	blood:	n/a	n/a
37	SMC3	chr12:116996479-116998008	GM12878	blood:	n/a	chr12:116997923-116997930
38	CEBPB	chr12:116996331-116998103	GM12878	blood:	n/a	n/a
39	POLR2A	chr12:116996266-116997866	K562	blood:	n/a	n/a
40	YY1	chr12:116996547-116997571	K562	blood:	n/a	chr12:116997125-116997144
41	RAD21	chr12:116996793-116997125	GM12878	blood:	n/a	n/a
42	TCF3	chr12:116996757-116997962	GM12878	blood:	n/a	n/a
43	PAX5	chr12:116996773-116997955	GM12878	blood:	n/a	chr12:116997680-116997699 chr12:116997629-116997638 chr12:116997085-116997112
44	BCL11A	chr12:116996823-116997162	GM12878	blood:	n/a	n/a
45	SP1	chr12:116996710-116997979	GM12878	blood:	n/a	chr12:116997638-116997652 chr12:116997557-116997570
46	ATF2	chr12:116996676-116998000	GM12878	blood:	n/a	n/a
47	BHLHE40	chr12:116996769-116997989	GM12878	blood:	n/a	n/a
48	RELA	chr12:116996400-116997993	GM18951	blood:	n/a	n/a
49	EP300	chr12:116996691-116997958	GM12878	blood:	n/a	chr12:116997517-116997527 chr12:116997875-116997889 chr12:116997832-116997846
50	FOXM1	chr12:116996483-116998045	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:116971915..116975712-chr12:116994698..116997472,3	MCF-7	breast:
2	chr12:116968953..116973759-chr12:116995509..116998903,7	K562	blood:

Variant related genes	Relation type
MAP1LC3B2	TF binding region
ENSG00000196668	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10850665	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068069	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12230564	0.82[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181730	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899540	chr12:116920503-116999861	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:116984200-116997000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:116993000-116997200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr12:116994600-116997400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:116994800-116997000	Enhancers	HMEC	breast
5	chr12:116994800-116997400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr12:116995000-116997200	Weak transcription	Fetal Brain Male	brain
7	chr12:116995200-116997000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:116995200-116997000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:116995200-116997600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr12:116995200-116999600	Enhancers	Fetal Muscle Leg	muscle
11	chr12:116995400-116997000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr12:116995400-116997000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr12:116995400-116997200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:116995400-116998000	Enhancers	Fetal Intestine Small	intestine
15	chr12:116995600-116997200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:116995600-116998400	Enhancers	Fetal Muscle Trunk	muscle
17	chr12:116996000-116997000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr12:116996000-116997200	Weak transcription	Right Atrium	heart
19	chr12:116996000-116998000	Enhancers	Fetal Intestine Large	intestine
20	chr12:116996200-116997000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:116996200-116997000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr12:116996200-116997000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:116996200-116997000	Enhancers	Adipose Nuclei	Adipose
24	chr12:116996200-116997200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:116996200-116997400	Flanking Active TSS	K562	blood
26	chr12:116996200-116997800	Flanking Active TSS	Dnd41	blood
27	chr12:116996200-116998000	Flanking Active TSS	Fetal Thymus	thymus
28	chr12:116996400-116997000	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr12:116996400-116997000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr12:116996400-116997000	Enhancers	Brain Hippocampus Middle	brain
31	chr12:116996400-116997200	Flanking Active TSS	Thymus	Thymus
32	chr12:116996400-116997400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr12:116996400-116997400	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr12:116996400-116997400	Flanking Active TSS	GM12878-XiMat	blood
35	chr12:116996400-116997400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr12:116996400-116997600	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr12:116996400-116997600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:116996400-116997600	Flanking Active TSS	HSMMtube	muscle
39	chr12:116996400-116997800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:116996400-116997800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr12:116996400-116997800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:116996400-116997800	Enhancers	Placenta	Placenta
43	chr12:116996400-116997800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr12:116996400-116997800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr12:116996400-116997800	Enhancers	Stomach Mucosa	stomach
46	chr12:116996400-116997800	Enhancers	NH-A	brain
47	chr12:116996400-116998000	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr12:116996400-116998000	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr12:116996400-116998000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr12:116996600-116997000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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