Variant report

Variant	rs12199296
Chromosome Location	chr6:144417730-144417731
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:144414988-144417802	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:144416048-144417814	GM12892	blood:	n/a	n/a
3	POLR2A	chr6:144416230-144417742	K562	blood:	n/a	n/a
4	PML	chr6:144416231-144417906	GM12878	blood:	n/a	n/a
5	TBL1XR1	chr6:144417392-144417740	GM12878	blood:	n/a	n/a
6	FOXM1	chr6:144416201-144417751	GM12878	blood:	n/a	n/a
7	KAP1	chr6:144416290-144417787	HEK293	kidney:	n/a	n/a
8	RUNX3	chr6:144416250-144417752	GM12878	blood:	n/a	n/a
9	CREB1	chr6:144416160-144417822	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:144416041-144417795	K562	blood:	n/a	n/a
11	RUNX3	chr6:144416257-144417772	GM12878	blood:	n/a	n/a
12	TEAD4	chr6:144417251-144417798	K562	blood:	n/a	n/a
13	POLR2A	chr6:144416167-144417778	GM12878	blood:	n/a	n/a
14	TBP	chr6:144417448-144417800	GM12878	blood:	n/a	n/a
15	MTA3	chr6:144416126-144417740	GM12878	blood:	n/a	n/a
16	MAZ	chr6:144415916-144418179	IMR90	lung:	n/a	chr6:144416866-144416876
17	POLR2A	chr6:144415885-144417806	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr6:144414734-144417777	GM12891	blood:	n/a	n/a
19	MXI1	chr6:144415518-144417847	SK-N-SH	brain:	n/a	chr6:144416840-144416855
20	KAP1	chr6:144417424-144417749	U2OS	brain:	n/a	n/a
21	POLR2A	chr6:144415169-144417926	PBDE	blood:	n/a	n/a
22	ELF1	chr6:144416250-144417797	MCF-7	breast:	n/a	chr6:144417001-144417010 chr6:144416999-144417012 chr6:144416804-144416813
23	RCOR1	chr6:144416304-144417760	K562	blood:	n/a	n/a
24	POLR2A	chr6:144417425-144417738	MCF-7	breast:	n/a	n/a
25	POLR2A	chr6:144415788-144417753	GM18505	blood:	n/a	n/a
26	MXI1	chr6:144417495-144417794	GM12878	blood:	n/a	n/a
27	RFX5	chr6:144416145-144418192	SK-N-SH	brain:	n/a	n/a
28	ATF2	chr6:144417177-144417813	GM12878	blood:	n/a	n/a
29	TEAD4	chr6:144417473-144417782	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:144384404..144388265-chr6:144412934..144418087,11	K562	blood:
2	chr6:144417405..144419567-chr6:144536912..144538787,2	MCF-7	breast:
3	chr6:144384139..144386162-chr6:144415974..144418368,2	MCF-7	breast:
4	chr6:144382193..144387951-chr6:144413760..144419366,13	K562	blood:
5	chr6:143998944..144000506-chr6:144415343..144418005,2	K562	blood:
6	chr6:144417225..144419515-chr6:144583886..144585730,2	MCF-7	breast:

No data

Variant related genes	Relation type
SF3B5	TF binding region
ENSG00000112419	Chromatin interaction
ENSG00000118495	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12203051	0.90[MEX][hapmap]
rs17073326	0.88[ASN][1000 genomes]
rs17073339	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2092338	1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs2223498	0.84[CHB][hapmap]
rs2328544	0.95[ASN][1000 genomes]
rs2876581	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4895628	0.81[ASN][1000 genomes]
rs4896695	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	nsv886738	chr6:144387698-144428387	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144414800-144418000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:144415200-144417800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:144415400-144417800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:144415400-144417800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr6:144415400-144417800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:144415600-144417800	Active TSS	H1 Cell Line	embryonic stem cell
7	chr6:144415600-144417800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:144415600-144418200	Active TSS	Fetal Kidney	kidney
9	chr6:144415800-144417800	Active TSS	Muscle Satellite Cultured Cells	--
10	chr6:144415800-144417800	Active TSS	Fetal Intestine Large	intestine
11	chr6:144415800-144417800	Active TSS	Fetal Intestine Small	intestine
12	chr6:144415800-144417800	Active TSS	HSMMtube	muscle
13	chr6:144415800-144417800	Active TSS	NHLF	lung
14	chr6:144416000-144417800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:144416000-144417800	Active TSS	NH-A	brain
16	chr6:144416000-144418200	Active TSS	Fetal Lung	lung
17	chr6:144416200-144417800	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr6:144416200-144417800	Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr6:144416200-144417800	Active TSS	Brain Angular Gyrus	brain
20	chr6:144416200-144417800	Active TSS	Duodenum Mucosa	Duodenum
21	chr6:144416200-144417800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr6:144416200-144417800	Active TSS	Rectal Smooth Muscle	rectum
23	chr6:144416200-144417800	Active TSS	Thymus	Thymus
24	chr6:144416400-144417800	Active TSS	Colonic Mucosa	Colon
25	chr6:144416400-144417800	Active TSS	Fetal Brain Female	brain
26	chr6:144416600-144417800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:144417200-144417800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr6:144417200-144417800	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr6:144417200-144417800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr6:144417200-144417800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr6:144417200-144417800	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr6:144417200-144417800	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr6:144417200-144417800	Flanking Active TSS	Dnd41	blood
34	chr6:144417200-144417800	Flanking Active TSS	HMEC	breast
35	chr6:144417200-144417800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr6:144417400-144417800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr6:144417400-144417800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr6:144417400-144417800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr6:144417400-144417800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:144417400-144417800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:144417400-144417800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:144417400-144417800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:144417400-144417800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:144417400-144417800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:144417400-144417800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:144417400-144417800	Flanking Active TSS	Liver	Liver
47	chr6:144417400-144417800	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr6:144417400-144417800	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr6:144417400-144417800	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr6:144417400-144417800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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