Variant report

Variant	rs16857843
Chromosome Location	chr2:11884231-11884232
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	ATF2	chr2:11883996-11884600	H1-hESC	embryonic stem cell:	n/a	n/a
2	BHLHE40	chr2:11884028-11884623	K562	blood:	n/a	n/a
3	TBP	chr2:11884179-11884537	HepG2	liver:	n/a	n/a
4	NR2F2	chr2:11884065-11884607	K562	blood:	n/a	n/a
5	MAX	chr2:11884009-11884672	SK-N-SH	brain:	n/a	n/a
6	CEBPB	chr2:11883977-11884703	GM12878	blood:	n/a	n/a
7	MAZ	chr2:11884013-11885624	K562	blood:	n/a	n/a
8	FOXA2	chr2:11884169-11884650	HepG2	liver:	n/a	n/a
9	FOSL1	chr2:11883901-11884755	HCT-116	colon:	n/a	chr2:11884384-11884396 chr2:11884385-11884395 chr2:11884385-11884395 chr2:11884386-11884394 chr2:11884299-11884310 chr2:11884385-11884395
10	RCOR1	chr2:11883701-11885172	IMR90	lung:	n/a	n/a
11	SETDB1	chr2:11884007-11884515	U2OS	brain:	n/a	n/a
12	PML	chr2:11883938-11884615	K562	blood:	n/a	n/a
13	CEBPB	chr2:11884003-11884461	ECC-1	luminal epithelium:	n/a	n/a
14	TCF12	chr2:11883940-11884675	A549	lung:	n/a	n/a
15	RFX5	chr2:11884169-11884582	GM12878	blood:	n/a	n/a
16	BCL3	chr2:11883883-11884682	A549	lung:	n/a	n/a
17	ELF1	chr2:11884162-11884705	GM12878	blood:	n/a	n/a
18	USF1	chr2:11883978-11884617	A549	lung:	n/a	n/a
19	MTA3	chr2:11883841-11884692	GM12878	blood:	n/a	n/a
20	IRF4	chr2:11884038-11884638	GM12878	blood:	n/a	chr2:11884490-11884504
21	EP300	chr2:11884033-11885602	K562	blood:	n/a	chr2:11884174-11884181
22	TBL1XR1	chr2:11884007-11884639	K562	blood:	n/a	n/a
23	RCOR1	chr2:11883662-11884721	K562	blood:	n/a	n/a
24	POLR2A	chr2:11884063-11884759	HUVEC	blood vessel:	n/a	n/a
25	SMC3	chr2:11884121-11884515	K562	blood:	n/a	n/a
26	SP1	chr2:11884098-11884685	GM12878	blood:	n/a	chr2:11884267-11884281
27	POLR2A	chr2:11884083-11884675	U87	brain:	n/a	n/a
28	YY1	chr2:11884120-11884552	K562	blood:	n/a	n/a
29	STAT3	chr2:11883989-11884497	MCF10A-Er-Src	breast:	n/a	chr2:11884062-11884070 chr2:11884062-11884085
30	CEBPB	chr2:11884024-11884533	A549	lung:	n/a	n/a
31	ZNF384	chr2:11884089-11884583	K562	blood:	n/a	n/a
32	FOSL2	chr2:11883960-11884635	A549	lung:	n/a	chr2:11884384-11884396 chr2:11884385-11884395 chr2:11884385-11884395 chr2:11884386-11884394 chr2:11884300-11884311 chr2:11884385-11884395
33	FOSL1	chr2:11883773-11885150	HCT-116	colon:	n/a	chr2:11884384-11884396 chr2:11884385-11884395 chr2:11884385-11884395 chr2:11884386-11884394 chr2:11884299-11884310 chr2:11883863-11883874 chr2:11884385-11884395
34	ZKSCAN1	chr2:11884068-11884685	Hela-S3	cervix:	n/a	n/a
35	BHLHE40	chr2:11884047-11884587	GM12878	blood:	n/a	n/a
36	TCF7L2	chr2:11884089-11884624	PANC-1	pancreas:	n/a	n/a
37	RELA	chr2:11884161-11884654	GM18951	blood:	n/a	n/a
38	ELK1	chr2:11883881-11884594	Hela-S3	cervix:	n/a	n/a
39	TEAD4	chr2:11883821-11884690	K562	blood:	n/a	n/a
40	MAFK	chr2:11884137-11885467	HepG2	liver:	n/a	chr2:11884687-11884698 chr2:11884920-11884931 chr2:11884921-11884932 chr2:11884920-11884931 chr2:11884921-11884932 chr2:11884916-11884931
41	PAX5	chr2:11884195-11884577	GM12878	blood:	n/a	n/a
42	POLR2A	chr2:11883998-11884543	Hela-S3	cervix:	n/a	n/a
43	GABPA	chr2:11883920-11884642	A549	lung:	n/a	n/a
44	SIN3AK20	chr2:11884218-11884518	SK-N-SH	brain:	n/a	n/a
45	ZBTB33	chr2:11884020-11884542	A549	lung:	n/a	n/a
46	JUND	chr2:11884083-11884577	H1-hESC	embryonic stem cell:	n/a	chr2:11884384-11884396 chr2:11884385-11884395 chr2:11884385-11884395 chr2:11884386-11884394 chr2:11884384-11884395 chr2:11884385-11884395
47	POLR2A	chr2:11884220-11884306	ProgFib	skin:	n/a	n/a
48	USF1	chr2:11883955-11884553	ECC-1	luminal epithelium:	n/a	n/a
49	BCL11A	chr2:11884071-11884592	GM12878	blood:	n/a	n/a
50	NFIC	chr2:11884042-11884572	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11883702..11885372-chr2:11901343..11903845,2	K562	blood:
2	chr2:11881178..11885762-chr2:11886043..11889477,7	MCF-7	breast:
3	chr2:11882438..11884776-chr2:11910789..11914613,4	K562	blood:
4	chr2:11604833..11608003-chr2:11882353..11886330,4	K562	blood:
5	chr2:11882411..11885202-chr2:11902345..11904670,2	K562	blood:

Variant related genes	Relation type
LPIN1	TF binding region
ENSG00000134324	Chromatin interaction
ENSG00000169016	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16855583	0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16857840	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4076516	0.95[AFR][1000 genomes]
rs73181399	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73183104	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73183109	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73183116	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73183118	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73183119	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73183121	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73185104	0.95[AFR][1000 genomes]
rs871674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs893351	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv580973	chr2:11864946-11898931	Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv580974	chr2:11867841-11898931	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11879200-11884400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:11879800-11884400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:11881600-11884800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:11882000-11884400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:11882200-11884400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:11882200-11884400	Enhancers	Hela-S3	cervix
7	chr2:11882200-11884400	Enhancers	HMEC	breast
8	chr2:11882200-11884400	Enhancers	NHLF	lung
9	chr2:11882400-11884400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr2:11882400-11884400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:11882400-11884400	Enhancers	HUVEC	blood vessel
12	chr2:11882400-11886200	Enhancers	NHDF-Ad	bronchial
13	chr2:11882600-11885400	Flanking Bivalent TSS/Enh	HepG2	liver
14	chr2:11882600-11886800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:11882800-11885200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr2:11882800-11885400	Enhancers	Pancreas	Pancrea
17	chr2:11882800-11886000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:11882800-11886200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr2:11882800-11886400	Enhancers	Fetal Thymus	thymus
20	chr2:11882800-11886600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:11883000-11885200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr2:11883000-11885200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:11883000-11885200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:11883000-11885600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:11883000-11886200	Enhancers	Fetal Muscle Leg	muscle
26	chr2:11883200-11884400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:11883200-11884400	Flanking Active TSS	Liver	Liver
28	chr2:11883200-11884400	Enhancers	Fetal Muscle Trunk	muscle
29	chr2:11883200-11885000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr2:11883200-11885400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:11883200-11886000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:11883400-11885600	Flanking Active TSS	K562	blood
33	chr2:11883400-11886200	Enhancers	Fetal Intestine Large	intestine
34	chr2:11883400-11886200	Enhancers	Fetal Intestine Small	intestine
35	chr2:11883400-11886400	Enhancers	Fetal Heart	heart
36	chr2:11883400-11886400	Enhancers	Stomach Mucosa	stomach
37	chr2:11883400-11887000	Enhancers	Placenta	Placenta
38	chr2:11883600-11884400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:11883600-11884400	Enhancers	NHEK	skin
40	chr2:11883600-11884800	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr2:11883600-11885800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr2:11883600-11886200	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr2:11883600-11886200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:11883600-11886200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:11883600-11886400	Enhancers	Primary B cells from peripheral blood	blood
46	chr2:11883600-11886400	Enhancers	Ovary	ovary
47	chr2:11883600-11886400	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr2:11883600-11886800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:11883800-11884400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:11883800-11884400	Weak transcription	Small Intestine	intestine

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