Variant report

Variant	rs9940164
Chromosome Location	chr16:80574306-80574307
allele	A/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	CBX3	chr16:80574273-80574937	K562	blood:	n/a	n/a
2	POLR2A	chr16:80574278-80574923	GM12891	blood:	n/a	n/a
3	POLR2A	chr16:80574232-80575002	Hela-S3	cervix:	n/a	n/a
4	HDAC2	chr16:80574290-80575288	MCF-7	breast:	n/a	chr16:80574838-80574847
5	MAX	chr16:80574230-80575172	HepG2	liver:	n/a	n/a
6	POLR2A	chr16:80574165-80575113	GM12892	blood:	n/a	n/a
7	USF1	chr16:80574294-80574855	A549	lung:	n/a	n/a
8	GABPA	chr16:80574300-80575106	HL-60	blood:	n/a	chr16:80574841-80574855 chr16:80574844-80574853 chr16:80574844-80574855 chr16:80574844-80574858
9	POLR2A	chr16:80574230-80575036	GM12892	blood:	n/a	n/a
10	POLR2A	chr16:80574302-80574999	GM12878	blood:	n/a	n/a
11	ELF1	chr16:80574258-80575301	MCF-7	breast:	n/a	n/a
12	POLR2A	chr16:80574304-80575104	GM19193	blood:	n/a	n/a
13	POLR2A	chr16:80574278-80575003	Hela-S3	cervix:	n/a	n/a
14	MAFK	chr16:80574157-80575013	Hela-S3	cervix:	n/a	chr16:80574608-80574619 chr16:80574606-80574620 chr16:80574605-80574614 chr16:80574873-80574888 chr16:80574603-80574618 chr16:80574607-80574618
15	E2F6	chr16:80574148-80575095	A549	lung:	n/a	chr16:80574957-80574966 chr16:80574845-80574854 chr16:80574706-80574717
16	GABPA	chr16:80574171-80575128	A549	lung:	n/a	chr16:80574841-80574855 chr16:80574844-80574853 chr16:80574844-80574855 chr16:80574844-80574858
17	CHD1	chr16:80574104-80575329	IMR90	lung:	n/a	n/a
18	USF2	chr16:80574301-80574800	Hela-S3	cervix:	n/a	n/a
19	MYC	chr16:80574177-80574985	K562	blood:	n/a	n/a
20	MAX	chr16:80574301-80575044	Hela-S3	cervix:	n/a	n/a
21	ELF1	chr16:80574006-80575456	MCF-7	breast:	n/a	chr16:80574214-80574225
22	POLR2A	chr16:80574224-80575037	MCF-7	breast:	n/a	n/a
23	MAZ	chr16:80574186-80575078	Hela-S3	cervix:	n/a	n/a
24	GABPA	chr16:80574126-80575051	A549	lung:	n/a	chr16:80574841-80574855 chr16:80574844-80574853 chr16:80574844-80574855 chr16:80574844-80574858
25	E2F6	chr16:80574196-80575110	H1-hESC	embryonic stem cell:	n/a	chr16:80574957-80574966 chr16:80574845-80574854 chr16:80574706-80574717
26	MAX	chr16:80574185-80575291	MCF-7	breast:	n/a	n/a
27	MTA3	chr16:80574023-80575071	GM12878	blood:	n/a	n/a
28	RFX5	chr16:80574264-80575040	Hela-S3	cervix:	n/a	chr16:80574893-80574902 chr16:80574609-80574617 chr16:80574889-80574903 chr16:80574891-80574905
29	POLR2A	chr16:80574304-80574925	GM12891	blood:	n/a	n/a
30	MAX	chr16:80574257-80575046	ECC-1	luminal epithelium:	n/a	n/a
31	TBP	chr16:80574261-80574960	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr16:80574302-80574906	GM12891	blood:	n/a	n/a
33	TFAP2C	chr16:80574295-80575003	Hela-S3	cervix:	n/a	chr16:80574536-80574545 chr16:80574499-80574514
34	SP1	chr16:80574272-80575084	A549	lung:	n/a	n/a
35	POLR2A	chr16:80574302-80575129	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr16:80574268-80575111	ProgFib	skin:	n/a	n/a
37	POLR2A	chr16:80574219-80574989	GM12878	blood:	n/a	n/a
38	SIN3AK20	chr16:80574228-80575401	MCF-7	breast:	n/a	n/a
39	POLR2A	chr16:80574215-80575190	PBDE	blood:	n/a	n/a
40	TBL1XR1	chr16:80574192-80575070	GM12878	blood:	n/a	n/a
41	RUNX3	chr16:80574297-80575044	GM12878	blood:	n/a	n/a
42	MXI1	chr16:80574087-80575463	SK-N-SH	brain:	n/a	chr16:80574579-80574594
43	TEAD4	chr16:80574287-80574944	K562	blood:	n/a	n/a
44	ELF1	chr16:80574299-80575195	GM12878	blood:	n/a	n/a
45	POLR2A	chr16:80573873-80574995	GM12891	blood:	n/a	n/a
46	TCF12	chr16:80574168-80575185	A549	lung:	n/a	chr16:80574759-80574769
47	MAZ	chr16:80574271-80575056	K562	blood:	n/a	n/a
48	TFAP2A	chr16:80574225-80574979	Hela-S3	cervix:	n/a	chr16:80574499-80574514
49	SIN3AK20	chr16:80574138-80575434	MCF-7	breast:	n/a	n/a
50	POLR2A	chr16:80574300-80574957	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:80573239..80577400-chr16:80578381..80583465,6	MCF-7	breast:
2	chr16:80573192..80575392-chr16:80605742..80608359,2	MCF-7	breast:
3	chr16:80573111..80574963-chr16:80576346..80580119,3	K562	blood:
4	chr16:80572758..80574587-chr16:80801032..80802655,2	MCF-7	breast:
5	chr16:80573487..80575142-chr16:80836688..80838672,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDYL2-6	chr16:80573869-80574385	XLOC_012019

Variant related genes	Relation type
DYNLRB2	TF binding region
ENSG00000260737	Chromatin interaction
ENSG00000166446	Chromatin interaction
ENSG00000168589	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11644889	0.87[ASN][1000 genomes]
rs11649558	0.87[ASN][1000 genomes]
rs11863816	0.87[ASN][1000 genomes]
rs11866588	0.87[ASN][1000 genomes]
rs11866734	0.87[ASN][1000 genomes]
rs12051207	0.87[ASN][1000 genomes]
rs12102506	0.87[ASN][1000 genomes]
rs12448344	0.93[CEU][hapmap]
rs12920691	0.86[EUR][1000 genomes]
rs12933306	0.86[EUR][1000 genomes]
rs28448585	0.87[ASN][1000 genomes]
rs28531767	0.87[ASN][1000 genomes]
rs28581872	0.87[ASN][1000 genomes]
rs28583998	0.87[ASN][1000 genomes]
rs28657821	0.87[ASN][1000 genomes]
rs28668848	0.87[ASN][1000 genomes]
rs28683132	0.87[ASN][1000 genomes]
rs28759267	0.87[ASN][1000 genomes]
rs4302045	0.87[ASN][1000 genomes]
rs4334316	0.87[ASN][1000 genomes]
rs59416398	0.87[ASN][1000 genomes]
rs7187807	1.00[ASN][1000 genomes]
rs73574263	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73574279	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928978	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9929079	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9931700	0.87[ASN][1000 genomes]
rs9932143	0.87[ASN][1000 genomes]
rs9933884	0.87[ASN][1000 genomes]
rs9937217	0.87[ASN][1000 genomes]
rs9972747	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907001	chr16:80405292-80620611	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv833300	chr16:80475066-80601036	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1060621	chr16:80532848-80980616	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv542989	chr16:80532848-80980616	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80573600-80574400	Active TSS	Primary hematopoietic stem cells	blood
2	chr16:80573800-80575000	Active TSS	Psoas Muscle	Psoas
3	chr16:80573800-80575000	Active TSS	Thymus	Thymus
4	chr16:80573800-80575400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr16:80574000-80574400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr16:80574000-80574400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr16:80574000-80574400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr16:80574000-80574400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr16:80574000-80574400	Flanking Active TSS	Brain Angular Gyrus	brain
10	chr16:80574000-80574400	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr16:80574000-80574400	Flanking Active TSS	Brain Substantia Nigra	brain
12	chr16:80574000-80574400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr16:80574000-80574600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr16:80574000-80574600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr16:80574000-80574600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr16:80574000-80574600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr16:80574000-80574600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr16:80574000-80574600	Flanking Active TSS	Liver	Liver
19	chr16:80574000-80574600	Flanking Active TSS	Rectal Smooth Muscle	rectum
20	chr16:80574000-80574600	Flanking Active TSS	A549	lung
21	chr16:80574000-80574600	Flanking Active TSS	NHEK	skin
22	chr16:80574000-80575000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr16:80574000-80575200	Active TSS	Brain Hippocampus Middle	brain
24	chr16:80574000-80575200	Active TSS	K562	blood
25	chr16:80574000-80575400	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr16:80574000-80575400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr16:80574000-80575400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr16:80574000-80575400	Active TSS	Muscle Satellite Cultured Cells	--
29	chr16:80574000-80575400	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr16:80574000-80575400	Active TSS	Right Atrium	heart
31	chr16:80574000-80575400	Active TSS	Stomach Smooth Muscle	stomach
32	chr16:80574000-80575600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr16:80574000-80575600	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr16:80574000-80575600	Active TSS	HSMMtube	muscle
35	chr16:80574200-80574400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr16:80574200-80574400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr16:80574200-80574400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr16:80574200-80574400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr16:80574200-80574400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr16:80574200-80574400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr16:80574200-80574400	Active TSS	Colonic Mucosa	Colon
42	chr16:80574200-80574400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr16:80574200-80574400	Active TSS	Fetal Muscle Trunk	muscle
44	chr16:80574200-80574400	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr16:80574200-80574400	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr16:80574200-80574400	Active TSS	Osteobl	bone
47	chr16:80574200-80574600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
48	chr16:80574200-80574600	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr16:80574200-80574600	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr16:80574200-80574600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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