Variant report

Variant	rs9922406
Chromosome Location	chr16:80574886-80574887
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	ZBTB33	chr16:80574445-80574991	A549	lung:	n/a	n/a
2	TAF1	chr16:80574389-80574902	GM12891	blood:	n/a	n/a
3	BCLAF1	chr16:80574333-80574994	GM12878	blood:	n/a	n/a
4	SMC3	chr16:80574337-80575125	Hela-S3	cervix:	n/a	chr16:80574587-80574601 chr16:80575095-80575102 chr16:80575076-80575086
5	CBX3	chr16:80574273-80574937	K562	blood:	n/a	n/a
6	POLR2A	chr16:80574316-80575027	U87	brain:	n/a	n/a
7	GABPA	chr16:80574379-80574988	HepG2	liver:	n/a	chr16:80574841-80574855 chr16:80574844-80574853 chr16:80574844-80574855 chr16:80574844-80574858
8	E2F6	chr16:80574367-80575094	K562	blood:	n/a	chr16:80574957-80574966 chr16:80574845-80574854 chr16:80574706-80574717
9	HEY1	chr16:80574508-80574898	K562	blood:	n/a	n/a
10	POLR2A	chr16:80574278-80574923	GM12891	blood:	n/a	n/a
11	ELF1	chr16:80574473-80575128	SK-N-SH	brain:	n/a	n/a
12	HCFC1	chr16:80574413-80575028	K562	blood:	n/a	n/a
13	NFYB	chr16:80574527-80574891	Hela-S3	cervix:	n/a	n/a
14	FOXA2	chr16:80574699-80575039	HepG2	liver:	n/a	n/a
15	SIN3AK20	chr16:80574633-80575105	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr16:80574481-80575091	HUVEC	blood vessel:	n/a	n/a
17	FOXA1	chr16:80574655-80575103	T-47D	breast:	n/a	n/a
18	POLR2A	chr16:80574232-80575002	Hela-S3	cervix:	n/a	n/a
19	EBF1	chr16:80574534-80575005	GM12878	blood:	n/a	n/a
20	POLR2A	chr16:80574395-80574898	SK-N-MC	brain:	n/a	n/a
21	TBL1XR1	chr16:80574455-80574950	K562	blood:	n/a	n/a
22	RCOR1	chr16:80574392-80575026	Hela-S3	cervix:	n/a	n/a
23	HDAC2	chr16:80574290-80575288	MCF-7	breast:	n/a	chr16:80574838-80574847
24	POLR2A	chr16:80574323-80575142	Hela-S3	cervix:	n/a	n/a
25	YY1	chr16:80574366-80574944	GM12878	blood:	n/a	n/a
26	GATA3	chr16:80574583-80575020	T-47D	breast:	n/a	n/a
27	MAX	chr16:80574230-80575172	HepG2	liver:	n/a	n/a
28	ELF1	chr16:80574332-80575104	K562	blood:	n/a	n/a
29	POLR2A	chr16:80574402-80575034	HL-60	blood:	n/a	n/a
30	YY1	chr16:80574396-80574925	SK-N-SH_RA	brain:	n/a	n/a
31	ETS1	chr16:80574534-80574986	A549	lung:	n/a	chr16:80574536-80574545 chr16:80574536-80574545 chr16:80574536-80574545 chr16:80574536-80574545 chr16:80574536-80574545 chr16:80574536-80574545
32	SIX5	chr16:80574529-80574923	A549	lung:	n/a	n/a
33	MYBL2	chr16:80574535-80575072	HepG2	liver:	n/a	n/a
34	POLR2A	chr16:80574165-80575113	GM12892	blood:	n/a	n/a
35	POLR2A	chr16:80574338-80575136	MCF-7	breast:	n/a	n/a
36	SIN3AK20	chr16:80574716-80575108	K562	blood:	n/a	n/a
37	SIN3A	chr16:80574520-80575068	GM12878	blood:	n/a	n/a
38	GABPA	chr16:80574300-80575106	HL-60	blood:	n/a	chr16:80574841-80574855 chr16:80574844-80574853 chr16:80574844-80574855 chr16:80574844-80574858
39	MAZ	chr16:80574495-80574995	HepG2	liver:	n/a	n/a
40	POLR2A	chr16:80574230-80575036	GM12892	blood:	n/a	n/a
41	SIN3A	chr16:80574392-80575304	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr16:80574407-80575164	H1-neurons	neurons:	n/a	n/a
43	MAX	chr16:80574372-80575031	K562	blood:	n/a	n/a
44	EP300	chr16:80574640-80574984	SK-N-SH_RA	brain:	n/a	chr16:80574878-80574887
45	POLR2A	chr16:80574547-80574926	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr16:80574457-80574900	GM12878	blood:	n/a	n/a
47	FOXP2	chr16:80574672-80575060	PFSK-1	brain:	n/a	n/a
48	CREB1	chr16:80574704-80574954	A549	lung:	n/a	n/a
49	E2F6	chr16:80574337-80575003	H1-hESC	embryonic stem cell:	n/a	chr16:80574957-80574966 chr16:80574845-80574854 chr16:80574706-80574717
50	POLR2A	chr16:80574302-80574999	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:80573239..80577400-chr16:80578381..80583465,6	MCF-7	breast:
2	chr16:80574441..80574962-chr2:58273829..58274361,2	Hela-S3	cervix:
3	chr16:80573192..80575392-chr16:80605742..80608359,2	MCF-7	breast:
4	chr16:80573111..80574963-chr16:80576346..80580119,3	K562	blood:
5	chr16:80573487..80575142-chr16:80836688..80838672,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259867	TF binding region
DYNLRB2	TF binding region
ENSG00000028116	Chromatin interaction
ENSG00000166446	Chromatin interaction
ENSG00000260737	Chromatin interaction
ENSG00000168589	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs4307962	0.92[LWK][hapmap]
rs4561480	1.00[ASW][hapmap];0.82[LWK][hapmap]
rs4622521	1.00[ASW][hapmap]
rs5012968	1.00[ASW][hapmap];0.92[LWK][hapmap];0.88[MKK][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes]
rs7196394	0.91[YRI][hapmap]
rs7197982	0.91[YRI][hapmap]
rs7202313	0.83[YRI][hapmap];0.89[AFR][1000 genomes]
rs7202484	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs8061925	1.00[ASW][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap]
rs8062532	1.00[ASW][hapmap];0.92[LWK][hapmap]

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	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
5	esv3431284	chr16:80574770-80575066	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9922406	CD3D	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80573800-80575000	Active TSS	Psoas Muscle	Psoas
2	chr16:80573800-80575000	Active TSS	Thymus	Thymus
3	chr16:80573800-80575400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr16:80574000-80575000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr16:80574000-80575200	Active TSS	Brain Hippocampus Middle	brain
6	chr16:80574000-80575200	Active TSS	K562	blood
7	chr16:80574000-80575400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr16:80574000-80575400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr16:80574000-80575400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr16:80574000-80575400	Active TSS	Muscle Satellite Cultured Cells	--
11	chr16:80574000-80575400	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr16:80574000-80575400	Active TSS	Right Atrium	heart
13	chr16:80574000-80575400	Active TSS	Stomach Smooth Muscle	stomach
14	chr16:80574000-80575600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr16:80574000-80575600	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr16:80574000-80575600	Active TSS	HSMMtube	muscle
17	chr16:80574200-80575000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr16:80574200-80575000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr16:80574200-80575000	Active TSS	Fetal Muscle Leg	muscle
20	chr16:80574200-80575000	Active TSS	Fetal Thymus	thymus
21	chr16:80574200-80575000	Active TSS	GM12878-XiMat	blood
22	chr16:80574200-80575200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr16:80574200-80575200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr16:80574200-80575200	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr16:80574200-80575200	Flanking Bivalent TSS/Enh	HepG2	liver
26	chr16:80574200-80575400	Active TSS	H9 Cell Line	embryonic stem cell
27	chr16:80574200-80575400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr16:80574200-80575400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr16:80574200-80575400	Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr16:80574200-80575400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr16:80574200-80575400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr16:80574200-80575400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr16:80574200-80575400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr16:80574200-80575400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr16:80574200-80575400	Active TSS	Colon Smooth Muscle	Colon
36	chr16:80574200-80575400	Active TSS	Fetal Brain Female	brain
37	chr16:80574200-80575400	Active TSS	Ovary	ovary
38	chr16:80574200-80575400	Active TSS	HSMM	muscle
39	chr16:80574200-80575400	Flanking Active TSS	HUVEC	blood vessel
40	chr16:80574200-80575400	Active TSS	NH-A	brain
41	chr16:80574200-80575400	Active TSS	NHDF-Ad	bronchial
42	chr16:80574200-80575400	Active TSS	NHLF	lung
43	chr16:80574200-80575600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr16:80574200-80575600	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr16:80574200-80575800	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr16:80574200-80575800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr16:80574200-80575800	Active TSS	Fetal Brain Male	brain
48	chr16:80574400-80575000	Active TSS	Pancreas	Pancrea
49	chr16:80574400-80575200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr16:80574400-80575200	Active TSS	HUES6 Cell Line	embryonic stem cell

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