Variant report

Variant	rs73949507
Chromosome Location	chr2:86667994-86667995
allele	C/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	POLR2A	chr2:86667700-86668762	GM12878	blood:	n/a	n/a
2	BRCA1	chr2:86667629-86668661	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:86667740-86668806	HCT-116	colon:	n/a	n/a
4	POLR2A	chr2:86667711-86669509	GM19193	blood:	n/a	n/a
5	POLR2A	chr2:86667884-86668138	SK-N-SH	brain:	n/a	n/a
6	TAF1	chr2:86667749-86668665	H1-neurons	neurons:	n/a	n/a
7	GABPA	chr2:86667828-86668557	A549	lung:	n/a	chr2:86667900-86667909 chr2:86667898-86667912 chr2:86667845-86667859 chr2:86667848-86667859 chr2:86667898-86667909
8	USF1	chr2:86667760-86668061	GM12878	blood:	n/a	n/a
9	MYBL2	chr2:86667284-86668677	HepG2	liver:	n/a	n/a
10	BCL3	chr2:86667389-86668439	A549	lung:	n/a	chr2:86667856-86667869
11	CEBPD	chr2:86667673-86668705	K562	blood:	n/a	n/a
12	CREB1	chr2:86667840-86668662	A549	lung:	n/a	n/a
13	CEBPB	chr2:86667846-86668566	IMR90	lung:	n/a	chr2:86668417-86668425
14	TAF1	chr2:86667692-86668659	A549	lung:	n/a	n/a
15	MAX	chr2:86667357-86668843	A549	lung:	n/a	chr2:86667843-86667850 chr2:86668345-86668355 chr2:86667840-86667855 chr2:86668553-86668563 chr2:86667838-86667853 chr2:86667842-86667852 chr2:86667842-86667851
16	POLR2A	chr2:86667655-86669884	GM19099	blood:	n/a	n/a
17	TEAD4	chr2:86667686-86668058	H1-hESC	embryonic stem cell:	n/a	n/a
18	NFYB	chr2:86667773-86668650	GM12878	blood:	n/a	chr2:86668414-86668429 chr2:86668416-86668426 chr2:86668414-86668429 chr2:86668414-86668428 chr2:86668413-86668425 chr2:86668411-86668426
19	POLR2A	chr2:86667739-86669701	H1-hESC	embryonic stem cell:	n/a	n/a
20	NR2F2	chr2:86667556-86668517	K562	blood:	n/a	n/a
21	EGR1	chr2:86667731-86668654	K562	blood:	n/a	chr2:86667849-86667858 chr2:86667899-86667908 chr2:86668347-86668360 chr2:86667976-86667990
22	POLR2A	chr2:86667840-86668736	H1-hESC	embryonic stem cell:	n/a	n/a
23	CEBPB	chr2:86667873-86668461	A549	lung:	n/a	chr2:86668417-86668425
24	CEBPB	chr2:86667748-86668598	H1-hESC	embryonic stem cell:	n/a	chr2:86668417-86668425
25	BACH1	chr2:86667542-86668688	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZNF143	chr2:86667513-86668627	GM12878	blood:	n/a	n/a
27	STAT5A	chr2:86667514-86668477	GM12878	blood:	n/a	chr2:86668304-86668316 chr2:86667969-86667981 chr2:86667974-86667986
28	MAX	chr2:86667223-86668388	GM12878	blood:	n/a	chr2:86667843-86667850 chr2:86668345-86668355 chr2:86667840-86667855 chr2:86667838-86667853 chr2:86667842-86667852 chr2:86667842-86667851
29	USF1	chr2:86667597-86668040	H1-hESC	embryonic stem cell:	n/a	n/a
30	EBF1	chr2:86667625-86668493	GM12878	blood:	n/a	n/a
31	REST	chr2:86667821-86668348	PFSK-1	brain:	n/a	chr2:86667855-86667868 chr2:86667997-86668010
32	POLR2A	chr2:86667642-86668700	U87	brain:	n/a	n/a
33	FOSL2	chr2:86667616-86668655	A549	lung:	n/a	chr2:86668542-86668552 chr2:86668543-86668551 chr2:86668445-86668454 chr2:86668542-86668552 chr2:86668558-86668567 chr2:86668418-86668427 chr2:86668551-86668560
34	MAX	chr2:86667545-86668758	MCF-7	breast:	n/a	chr2:86667843-86667850 chr2:86668345-86668355 chr2:86667840-86667855 chr2:86668553-86668563 chr2:86667838-86667853 chr2:86667842-86667852 chr2:86667842-86667851
35	NFIC	chr2:86667323-86668504	GM12878	blood:	n/a	n/a
36	TEAD4	chr2:86667448-86668388	K562	blood:	n/a	n/a
37	MAX	chr2:86667556-86668605	A549	lung:	n/a	chr2:86667843-86667850 chr2:86668345-86668355 chr2:86667840-86667855 chr2:86668553-86668563 chr2:86667838-86667853 chr2:86667842-86667852 chr2:86667842-86667851
38	ZNF384	chr2:86667740-86668605	K562	blood:	n/a	n/a
39	REST	chr2:86667722-86668333	K562	blood:	n/a	chr2:86667855-86667868 chr2:86667997-86668010
40	MYC	chr2:86667783-86668075	MCF-7	breast:	n/a	chr2:86667843-86667850 chr2:86667840-86667855 chr2:86667838-86667853 chr2:86667842-86667852 chr2:86667842-86667851
41	JUND	chr2:86667582-86668681	H1-hESC	embryonic stem cell:	n/a	chr2:86668542-86668552 chr2:86668543-86668551 chr2:86668445-86668454 chr2:86668542-86668552 chr2:86668558-86668567 chr2:86668418-86668427 chr2:86668551-86668560
42	USF2	chr2:86667645-86668256	GM12878	blood:	n/a	n/a
43	USF1	chr2:86667592-86668119	ECC-1	luminal epithelium:	n/a	n/a
44	MYC	chr2:86667668-86668572	K562	blood:	n/a	chr2:86667843-86667850 chr2:86668345-86668355 chr2:86667840-86667855 chr2:86668553-86668563 chr2:86667838-86667853 chr2:86667842-86667852 chr2:86667842-86667851
45	POLR2A	chr2:86667695-86669559	GM12892	blood:	n/a	n/a
46	STAT3	chr2:86667492-86668271	GM12878	blood:	n/a	chr2:86667969-86667981 chr2:86667974-86667986
47	POLR2A	chr2:86667781-86668130	GM12878	blood:	n/a	n/a
48	USF1	chr2:86667633-86668185	A549	lung:	n/a	n/a
49	STAT5A	chr2:86667823-86668432	GM12878	blood:	n/a	chr2:86668304-86668316 chr2:86667969-86667981 chr2:86667974-86667986
50	MYC	chr2:86667407-86669561	K562	blood:	n/a	chr2:86669091-86669101 chr2:86667843-86667850 chr2:86668345-86668355 chr2:86667840-86667855 chr2:86668553-86668563 chr2:86667838-86667853 chr2:86667842-86667852 chr2:86667842-86667851

No.	Distal block	Cell Line	Cell type
1	chr2:86667340..86669262-chr2:86848703..86850957,2	MCF-7	breast:
2	chr2:85644431..85647240-chr2:86667731..86670079,2	MCF-7	breast:
3	chr2:86667710..86668832-chr6:27100599..27101496,3	Hela-S3	cervix:
4	chr2:86667867..86670714-chr2:86788591..86792016,6	K562	blood:
5	chr2:86667181..86671352-chr2:86788569..86792016,9	K562	blood:
6	chr2:86667874..86671580-chr2:86848738..86852940,5	K562	blood:
7	chr2:86666553..86668600-chr2:86715383..86717165,2	K562	blood:
8	chr2:86421282..86424146-chr2:86666466..86669906,3	K562	blood:
9	chr2:86421023..86423048-chr2:86667398..86669941,4	MCF-7	breast:

Variant related genes	Relation type
KDM3A	TF binding region
ENSG00000115561	Chromatin interaction
ENSG00000249884	Chromatin interaction
ENSG00000228363	Chromatin interaction
ENSG00000132305	Chromatin interaction
ENSG00000115548	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000273080	Chromatin interaction
ENSG00000239305	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000042493	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17027287	1.00[AMR][1000 genomes]
rs56249372	1.00[AMR][1000 genomes]
rs58376522	1.00[AMR][1000 genomes]
rs58487331	1.00[AMR][1000 genomes]
rs72928459	1.00[AMR][1000 genomes]
rs73945296	1.00[AMR][1000 genomes]
rs73946220	1.00[AMR][1000 genomes]
rs73949509	1.00[AMR][1000 genomes]
rs73949510	1.00[AMR][1000 genomes]
rs73949511	1.00[AMR][1000 genomes]
rs73949513	1.00[AMR][1000 genomes]
rs7557127	1.00[AMR][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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	esv3354834	chr2:86667466-86670414	Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86666600-86668200	Active TSS	Fetal Heart	heart
2	chr2:86666800-86668000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
3	chr2:86667000-86668200	Active TSS	Fetal Brain Male	brain
4	chr2:86667200-86668000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
5	chr2:86667200-86668000	ZNF genes & repeats	GM12878-XiMat	blood
6	chr2:86667400-86668000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:86667400-86669200	Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr2:86667400-86670000	Active TSS	Brain Anterior Caudate	brain
9	chr2:86667400-86670000	Active TSS	HMEC	breast
10	chr2:86667400-86670200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:86667400-86670200	Active TSS	Brain Cingulate Gyrus	brain
12	chr2:86667400-86670200	Active TSS	Brain Hippocampus Middle	brain
13	chr2:86667600-86668000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:86667600-86668000	ZNF genes & repeats	Fetal Intestine Large	intestine
15	chr2:86667600-86668200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:86667600-86669200	Active TSS	Primary hematopoietic stem cells	blood
17	chr2:86667600-86669200	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr2:86667600-86669200	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr2:86667600-86669200	Active TSS	Stomach Smooth Muscle	stomach
20	chr2:86667600-86669400	Active TSS	Liver	Liver
21	chr2:86667600-86669400	Active TSS	K562	blood
22	chr2:86667600-86669400	Active TSS	Monocytes-CD14+_RO01746	blood
23	chr2:86667600-86669600	Active TSS	Duodenum Mucosa	Duodenum
24	chr2:86667600-86669600	Active TSS	Osteobl	bone
25	chr2:86667600-86669800	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr2:86667600-86669800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:86667600-86669800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:86667600-86669800	Active TSS	Fetal Lung	lung
29	chr2:86667600-86670000	Active TSS	Primary T cells from cord blood	blood
30	chr2:86667600-86670000	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr2:86667600-86670000	Active TSS	A549	lung
32	chr2:86667600-86670200	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr2:86667600-86670200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:86667600-86670200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:86667600-86670200	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr2:86667600-86670200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:86667600-86670200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:86667600-86670200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:86667600-86670200	Active TSS	Brain Substantia Nigra	brain
40	chr2:86667600-86670200	Active TSS	Fetal Brain Female	brain
41	chr2:86667600-86670200	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr2:86667600-86670200	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr2:86667600-86670200	Active TSS	Thymus	Thymus
44	chr2:86667600-86670200	Active TSS	HSMM	muscle
45	chr2:86667600-86670400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:86667600-86670400	Active TSS	Brain Germinal Matrix	brain
47	chr2:86667600-86670400	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr2:86667600-86670400	Active TSS	Fetal Intestine Small	intestine
49	chr2:86667600-86670400	Active TSS	HSMMtube	muscle
50	chr2:86667600-86670800	Active TSS	Colonic Mucosa	Colon

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