Variant report

Variant	rs17041928
Chromosome Location	chr2:111966491-111966492
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	NFIC	chr2:111966432-111967114	GM12878	blood:	n/a	n/a
2	STAT1	chr2:111965967-111967091	GM12878	blood:	n/a	chr2:111966567-111966578
3	EBF1	chr2:111966244-111967098	GM12878	blood:	n/a	n/a
4	RUNX3	chr2:111966280-111967157	GM12878	blood:	n/a	n/a
5	WRNIP1	chr2:111965966-111967108	GM12878	blood:	n/a	n/a
6	MAX	chr2:111966195-111967149	GM12878	blood:	n/a	n/a
7	NFE2	chr2:111966449-111966643	GM12878	blood:	n/a	n/a
8	PBX3	chr2:111966470-111967008	SK-N-SH	brain:	n/a	n/a
9	RUNX3	chr2:111966392-111967123	GM12878	blood:	n/a	n/a
10	ZNF384	chr2:111966243-111967121	GM12878	blood:	n/a	n/a
11	RELA	chr2:111966191-111967124	GM12878	blood:	n/a	n/a
12	RELA	chr2:111965881-111967171	GM18951	blood:	n/a	n/a
13	EP300	chr2:111966336-111967285	GM12878	blood:	n/a	chr2:111966594-111966608
14	TBL1XR1	chr2:111966154-111967178	GM12878	blood:	n/a	n/a
15	RELA	chr2:111966256-111967153	GM15510	blood:	n/a	n/a
16	RELA	chr2:111966328-111967169	GM12892	blood:	n/a	n/a
17	RELA	chr2:111966328-111967155	GM19193	blood:	n/a	n/a
18	STAT3	chr2:111966451-111967156	GM12878	blood:	n/a	chr2:111966567-111966578
19	ATF2	chr2:111966420-111967152	GM12878	blood:	n/a	n/a
20	IKZF1	chr2:111966421-111967054	GM12878	blood:	n/a	n/a
21	MEF2A	chr2:111966376-111967034	GM12878	blood:	n/a	chr2:111966466-111966480 chr2:111966461-111966482 chr2:111966468-111966479 chr2:111966588-111966596 chr2:111966623-111966638 chr2:111966466-111966481 chr2:111966624-111966639
22	EP300	chr2:111966249-111967147	GM12878	blood:	n/a	chr2:111966594-111966608
23	BHLHE40	chr2:111966256-111967171	GM12878	blood:	n/a	n/a
24	MEF2C	chr2:111966396-111967038	GM12878	blood:	n/a	chr2:111966466-111966480 chr2:111966461-111966482 chr2:111966468-111966479 chr2:111966588-111966596 chr2:111966623-111966638 chr2:111966466-111966481 chr2:111966624-111966639
25	TBP	chr2:111966354-111967141	GM12878	blood:	n/a	n/a
26	MTA3	chr2:111966415-111967194	GM12878	blood:	n/a	n/a
27	BCLAF1	chr2:111966426-111967083	GM12878	blood:	n/a	n/a
28	RELA	chr2:111966269-111967161	GM12891	blood:	n/a	n/a
29	RCOR1	chr2:111966193-111967181	GM12878	blood:	n/a	n/a
30	PAX5	chr2:111966481-111967137	GM12878	blood:	n/a	n/a
31	NFATC1	chr2:111966446-111967039	GM12878	blood:	n/a	n/a
32	FOXM1	chr2:111966488-111967157	GM12878	blood:	n/a	n/a
33	FOXM1	chr2:111966477-111967004	GM12878	blood:	n/a	n/a
34	MEF2A	chr2:111966399-111967092	GM12878	blood:	n/a	chr2:111966466-111966480 chr2:111966461-111966482 chr2:111966468-111966479 chr2:111966588-111966596 chr2:111966623-111966638 chr2:111966466-111966481 chr2:111966624-111966639
35	SMC3	chr2:111966411-111967293	GM12878	blood:	n/a	n/a
36	POU2F2	chr2:111966270-111967126	GM12878	blood:	n/a	chr2:111966959-111966969 chr2:111966957-111966970 chr2:111966954-111966975 chr2:111966957-111966971 chr2:111966956-111966971 chr2:111966958-111966968 chr2:111966958-111966968 chr2:111966959-111966968 chr2:111966957-111966969 chr2:111966955-111966973 chr2:111966960-111966968 chr2:111966960-111966967 chr2:111966959-111966970
37	TCF12	chr2:111966434-111967113	SK-N-SH	brain:	n/a	n/a
38	RELA	chr2:111966439-111967188	GM10847	blood:	n/a	n/a
39	FOSL2	chr2:111966489-111966980	SK-N-SH	brain:	n/a	n/a
40	ATF2	chr2:111966356-111967056	GM12878	blood:	n/a	n/a
41	CHD2	chr2:111966333-111967157	GM12878	blood:	n/a	n/a
42	RELA	chr2:111966298-111967179	GM19099	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111876826..111879311-chr2:111966028..111968773,2	K562	blood:
2	chr2:111963419..111965229-chr2:111965718..111968351,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC108463.1-3	chr2:111966333-111966554	NONHSAT073620
2	lnc-AC108463.1-3	chr2:111965991-111966616	NONHSAT073625
3	lnc-AC108463.1-3	chr2:111965592-111966694	ENSG00000172965.10

Variant related genes	Relation type
ENSG00000227992	TF binding region
ENSG00000153094	Chromatin interaction
ENSG00000227992	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1464021	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17041943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17041945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs950471	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1803356	chr2:111899783-112662597	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv428402	chr2:111899783-112662597	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111950200-111969600	Weak transcription	Dnd41	blood
2	chr2:111952200-111974800	Weak transcription	Aorta	Aorta
3	chr2:111953000-111968000	Weak transcription	K562	blood
4	chr2:111954800-112006800	Weak transcription	HUVEC	blood vessel
5	chr2:111957200-111972400	Weak transcription	NHLF	lung
6	chr2:111958000-111974400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:111958400-111967600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:111958400-111968600	Weak transcription	HepG2	liver
9	chr2:111958400-111972000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:111958400-111974200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:111962600-111974400	Weak transcription	Left Ventricle	heart
12	chr2:111964600-111966600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:111964800-111967800	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:111965600-111967600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:111966000-111966600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:111966000-111967200	Enhancers	Primary B cells from peripheral blood	blood
17	chr2:111966200-111966600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:111966200-111966600	Weak transcription	HSMMtube	muscle
19	chr2:111966200-111967000	Enhancers	Osteobl	bone
20	chr2:111966200-111967200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:111966200-111967200	Enhancers	NH-A	brain
22	chr2:111966200-111969400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:111966200-111971800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:111966200-111974400	Weak transcription	Lung	lung
25	chr2:111966400-111966600	Flanking Active TSS	GM12878-XiMat	blood
26	chr2:111966400-111966800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:111966400-111967000	Enhancers	HMEC	breast
28	chr2:111966400-111967000	Enhancers	NHEK	skin
29	chr2:111966400-111967200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:111966400-111967200	Enhancers	HSMM	muscle
31	chr2:111966400-111968600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:111966400-111970600	Weak transcription	NHDF-Ad	bronchial
33	chr2:111966400-111974200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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