Variant report

Variant	rs17279967
Chromosome Location	chr3:100054490-100054491
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	HDAC2	chr3:100054355-100054663	K562	blood:	n/a	n/a
2	POLR2A	chr3:100053288-100054571	GM18526	blood:	n/a	n/a
3	POLR2A	chr3:100053973-100054744	K562	blood:	n/a	n/a
4	MYC	chr3:100053221-100054645	A549	lung:	n/a	chr3:100054520-100054529
5	RCOR1	chr3:100053387-100054933	K562	blood:	n/a	n/a
6	POLR2A	chr3:100053250-100054516	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr3:100052685-100054939	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:100054268-100054611	GM12878	blood:	n/a	n/a
9	RCOR1	chr3:100054311-100054511	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:100053313-100055020	K562	blood:	n/a	n/a
11	MXI1	chr3:100053218-100054515	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:100053059-100054674	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr3:100054380-100054530	GM12864	blood:	n/a	n/a
14	MXI1	chr3:100052857-100054783	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr3:100053112-100054666	GM12878	blood:	n/a	n/a
16	PBX3	chr3:100054284-100054533	GM12878	blood:	n/a	n/a
17	MAX	chr3:100054345-100054581	A549	lung:	n/a	chr3:100054520-100054529
18	SPI1	chr3:100054225-100054704	HL-60	blood:	n/a	chr3:100054380-100054389 chr3:100054504-100054511
19	MAFF	chr3:100053985-100054630	K562	blood:	n/a	n/a
20	SPI1	chr3:100054236-100054564	GM12891	blood:	n/a	chr3:100054380-100054389 chr3:100054504-100054511
21	CTCF	chr3:100054420-100054570	HBMEC	blood vessel:	n/a	n/a
22	POLR2A	chr3:100054267-100054700	GM12878	blood:	n/a	n/a
23	MAX	chr3:100054295-100054794	K562	blood:	n/a	chr3:100054520-100054529
24	RELA	chr3:100053197-100054532	GM15510	blood:	n/a	chr3:100054399-100054408 chr3:100054399-100054408
25	POLR2A	chr3:100054321-100054561	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr3:100053236-100054653	GM12891	blood:	n/a	n/a
27	MYC	chr3:100053366-100054557	MCF10A-Er-Src	breast:	n/a	chr3:100054520-100054529
28	POLR2A	chr3:100053276-100054688	HL-60	blood:	n/a	n/a
29	TBP	chr3:100053209-100054712	K562	blood:	n/a	n/a
30	POLR2A	chr3:100053155-100055087	GM12891	blood:	n/a	n/a
31	POLR2A	chr3:100054204-100054668	GM12891	blood:	n/a	n/a
32	POLR2A	chr3:100054389-100054694	MCF-7	breast:	n/a	n/a
33	ATF1	chr3:100054299-100054736	K562	blood:	n/a	n/a
34	MAX	chr3:100053086-100054743	NB4	blood:	n/a	chr3:100054520-100054529
35	POLR2A	chr3:100053228-100054809	GM19193	blood:	n/a	n/a
36	YY1	chr3:100054276-100054696	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:100053130-100054871	GM12892	blood:	n/a	n/a
38	HEY1	chr3:100053398-100054694	K562	blood:	n/a	n/a
39	POLR2A	chr3:100053275-100054529	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:100054147-100054756	HL-60	blood:	n/a	n/a
41	POLR2A	chr3:100053083-100054826	GM12892	blood:	n/a	n/a
42	POLR2A	chr3:100053262-100054565	GM12892	blood:	n/a	n/a
43	CBX3	chr3:100054244-100054908	K562	blood:	n/a	n/a
44	SIN3A	chr3:100052952-100054519	H1-hESC	embryonic stem cell:	n/a	n/a
45	SPI1	chr3:100054194-100054581	GM12878	blood:	n/a	chr3:100054380-100054389 chr3:100054504-100054511
46	POLR2A	chr3:100053142-100054796	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:100053176-100054783	GM12891	blood:	n/a	n/a
48	E2F6	chr3:100054210-100054757	K562	blood:	n/a	chr3:100054539-100054550
49	POLR2A	chr3:100053052-100055002	HepG2	liver:	n/a	n/a
50	POLR2A	chr3:100053320-100054599	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:100052434..100055247-chr3:100118351..100122265,5	K562	blood:
2	chr3:100051539..100055958-chr3:100056037..100061247,9	MCF-7	breast:
3	chr3:100052074..100055881-chr3:100116822..100121530,5	MCF-7	breast:

Variant related genes	Relation type
NIT2	TF binding region
ENSG00000154174	Chromatin interaction
ENSG00000114021	Chromatin interaction
ENSG00000206535	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1036768	0.85[EUR][1000 genomes]
rs1045610	0.83[EUR][1000 genomes]
rs10511179	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10936193	0.83[CEU][hapmap];0.90[TSI][hapmap]
rs11720172	0.82[EUR][1000 genomes]
rs11927693	0.83[EUR][1000 genomes]
rs12591	0.83[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs16842142	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs2068018	0.84[CEU][hapmap]
rs2289501	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs3772687	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs41272643	0.80[EUR][1000 genomes]
rs60028471	0.85[EUR][1000 genomes]
rs73150325	0.83[EUR][1000 genomes]
rs73150329	0.83[EUR][1000 genomes]
rs73150348	0.81[EUR][1000 genomes]
rs73150350	0.81[EUR][1000 genomes]
rs9873033	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17279967	TOMM70A	Cis_1M	lymphoblastoid	RTeQTL
rs17279967	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs17279967	NIT2	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100052800-100054600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:100052800-100054600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:100052800-100054800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:100052800-100054800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:100053000-100054600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:100053000-100054600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr3:100053000-100054600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:100053000-100054600	Active TSS	Rectal Smooth Muscle	rectum
9	chr3:100053000-100054600	Active TSS	HSMM	muscle
10	chr3:100053400-100054600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:100053400-100054800	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr3:100053400-100054800	Active TSS	Osteobl	bone
13	chr3:100054000-100054600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:100054000-100054600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:100054000-100054600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr3:100054000-100054600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:100054000-100054600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr3:100054000-100054600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:100054000-100054600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr3:100054000-100054600	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr3:100054000-100054600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr3:100054000-100054600	Flanking Active TSS	Fetal Muscle Leg	muscle
23	chr3:100054000-100054600	Flanking Active TSS	Placenta	Placenta
24	chr3:100054000-100054600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr3:100054000-100054600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr3:100054000-100054600	Flanking Active TSS	NH-A	brain
27	chr3:100054000-100054800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:100054000-100054800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr3:100054000-100054800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr3:100054000-100054800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:100054000-100054800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr3:100054000-100054800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:100054000-100054800	Flanking Active TSS	Liver	Liver
34	chr3:100054000-100054800	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr3:100054000-100054800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr3:100054000-100055000	Flanking Active TSS	Dnd41	blood
37	chr3:100054000-100065000	Weak transcription	Spleen	Spleen
38	chr3:100054200-100054600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
39	chr3:100054200-100054600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:100054200-100054600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr3:100054200-100054600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:100054200-100054600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr3:100054200-100054600	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr3:100054200-100054600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr3:100054200-100054600	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr3:100054200-100054600	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr3:100054200-100054600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr3:100054200-100054600	Flanking Active TSS	Fetal Brain Male	brain
49	chr3:100054200-100054600	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr3:100054200-100054600	Flanking Active TSS	NHLF	lung

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