Variant report

Variant	rs16949651
Chromosome Location	chr17:46019601-46019602
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	SP1	chr17:46018445-46019707	HepG2	liver:	n/a	chr17:46019208-46019217 chr17:46018864-46018875 chr17:46019246-46019255 chr17:46019209-46019218
2	CEBPB	chr17:46018651-46019609	HepG2	liver:	n/a	chr17:46018888-46018896
3	HNF4G	chr17:46018535-46019614	HepG2	liver:	n/a	chr17:46018961-46018969
4	POLR2A	chr17:46018328-46019666	GM12878	blood:	n/a	n/a
5	CREB1	chr17:46018233-46019893	HepG2	liver:	n/a	n/a
6	POLR2A	chr17:46018483-46020295	HepG2	liver:	n/a	n/a
7	EP300	chr17:46018386-46019888	HepG2	liver:	n/a	chr17:46019030-46019039
8	RFX5	chr17:46018121-46020592	SK-N-SH	brain:	n/a	chr17:46018887-46018896
9	SIX5	chr17:46018362-46020053	A549	lung:	n/a	n/a
10	MYBL2	chr17:46018324-46019664	HepG2	liver:	n/a	n/a
11	POLR2A	chr17:46018300-46019762	Raji	blood:	n/a	n/a
12	POLR2A	chr17:46019418-46019727	HepG2	liver:	n/a	n/a
13	POLR2A	chr17:46018370-46019792	GM12892	blood:	n/a	n/a
14	HEY1	chr17:46018447-46020067	HepG2	liver:	n/a	n/a
15	MAX	chr17:46018148-46019773	HCT-116	colon:	n/a	chr17:46019019-46019030 chr17:46019020-46019029 chr17:46019018-46019031 chr17:46019020-46019029
16	POLR2A	chr17:46018364-46019706	GM12891	blood:	n/a	n/a
17	RCOR1	chr17:46018305-46019654	HepG2	liver:	n/a	n/a
18	MYBL2	chr17:46018286-46019949	HepG2	liver:	n/a	n/a
19	ZBTB7A	chr17:46019544-46019825	K562	blood:	n/a	n/a
20	REST	chr17:46018177-46019781	A549	lung:	n/a	n/a
21	ARID3A	chr17:46018740-46019665	HepG2	liver:	n/a	n/a
22	HNF4G	chr17:46018665-46019895	HepG2	liver:	n/a	chr17:46018961-46018969
23	MXI1	chr17:46018405-46019639	Hela-S3	cervix:	n/a	chr17:46019019-46019028
24	POLR2A	chr17:46018386-46019976	HepG2	liver:	n/a	n/a
25	POLR2A	chr17:46018454-46019706	GM18505	blood:	n/a	n/a
26	CHD2	chr17:46019557-46019882	Hela-S3	cervix:	n/a	chr17:46019701-46019711
27	MAX	chr17:46018180-46020180	HCT-116	colon:	n/a	chr17:46019019-46019030 chr17:46019020-46019029 chr17:46019018-46019031 chr17:46019020-46019029
28	POLR2A	chr17:46018404-46019727	GM12892	blood:	n/a	n/a
29	FOXA2	chr17:46019243-46019626	HepG2	liver:	n/a	n/a
30	MAX	chr17:46018213-46019902	HepG2	liver:	n/a	chr17:46019019-46019030 chr17:46019020-46019029 chr17:46019018-46019031 chr17:46019020-46019029
31	PML	chr17:46018482-46019678	MCF-7	breast:	n/a	chr17:46018795-46018803
32	POLR2A	chr17:46018461-46019672	HCT-116	colon:	n/a	n/a
33	MBD4	chr17:46018343-46020002	HepG2	liver:	n/a	n/a
34	TCF12	chr17:46018224-46019728	A549	lung:	n/a	n/a
35	HNF4A	chr17:46018754-46019699	HepG2	liver:	n/a	chr17:46018961-46018969
36	TEAD4	chr17:46018457-46019754	HepG2	liver:	n/a	n/a
37	HNF4A	chr17:46018659-46019637	HepG2	liver:	n/a	chr17:46018961-46018969
38	MBD4	chr17:46018395-46019725	HepG2	liver:	n/a	n/a
39	SIN3AK20	chr17:46018220-46019917	MCF-7	breast:	n/a	n/a
40	MAX	chr17:46018360-46019608	HepG2	liver:	n/a	chr17:46019019-46019030 chr17:46019020-46019029 chr17:46019018-46019031 chr17:46019020-46019029
41	MTA3	chr17:46018904-46019658	GM12878	blood:	n/a	n/a
42	POLR2A	chr17:46018460-46019641	GM12891	blood:	n/a	n/a
43	POLR2A	chr17:46018481-46019779	GM19193	blood:	n/a	n/a
44	POLR2A	chr17:46018413-46019704	U87	brain:	n/a	n/a
45	HDAC2	chr17:46018512-46019761	HepG2	liver:	n/a	chr17:46018532-46018546
46	POLR2A	chr17:46018403-46019772	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr17:46018533-46020053	HepG2	liver:	n/a	n/a
48	BCL3	chr17:46018204-46019611	A549	lung:	n/a	chr17:46019209-46019218 chr17:46018664-46018673
49	TBP	chr17:46018570-46019632	HepG2	liver:	n/a	n/a
50	POLR2A	chr17:46018511-46019979	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:45970912..45974701-chr17:46018890..46021752,3	K562	blood:
2	chr17:46018061..46020719-chr17:46045036..46046879,2	K562	blood:
3	chr17:45915913..45917925-chr17:46018896..46020443,2	MCF-7	breast:
4	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
5	chr17:45915810..45917332-chr17:46018370..46020809,2	K562	blood:
6	chr17:45906214..45908869-chr17:46017254..46019863,3	MCF-7	breast:
7	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
8	chr17:45993643..45995953-chr17:46019014..46020704,3	MCF-7	breast:
9	chr17:45971510..45977679-chr17:46016123..46021422,20	MCF-7	breast:
10	chr17:46019148..46022019-chr17:46092699..46095180,2	K562	blood:
11	chr17:45978341..45980674-chr17:46019226..46022209,2	MCF-7	breast:
12	chr17:45973201..45977546-chr17:46016018..46021091,7	K562	blood:

Variant related genes	Relation type
ENSG00000263798	TF binding region
PNPO	TF binding region
ENSG00000234494	TF binding region
ENSG00000264920	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1133221	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16949270	1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs16949296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16949427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17616799	0.93[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1962201	0.87[ASN][1000 genomes]
rs1986694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2325750	0.87[CHB][hapmap];0.80[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2525105	0.86[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs3764393	0.89[ASN][1000 genomes]
rs4450442	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs55956628	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56006220	0.85[ASN][1000 genomes]
rs56402159	0.85[ASN][1000 genomes]
rs58848175	0.82[ASN][1000 genomes]
rs61396871	0.86[ASN][1000 genomes]
rs73323310	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9944405	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv2072	chr17:45998637-46019626	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16949651	CBX1	Cis_1M	lymphoblastoid	RTeQTL
rs16949651	CBX1	cis	cerebellum	SCAN
rs16949651	KRT37	cis	cerebellum	SCAN
rs16949651	CDK5RAP3	cis	cerebellum	SCAN
rs16949651	CDK5RAP3	cis	parietal	SCAN
rs16949651	KRTAP17-1	cis	cerebellum	SCAN
rs16949651	ASB16	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46018200-46020000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr17:46018200-46020000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:46018200-46020000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr17:46018200-46020000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr17:46018200-46020000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr17:46018200-46020000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr17:46018200-46020000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr17:46018200-46020200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:46018200-46020200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr17:46018400-46019800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr17:46018400-46020000	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr17:46018400-46020000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:46018600-46019800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr17:46018600-46019800	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr17:46018600-46019800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:46018600-46019800	Active TSS	Brain Angular Gyrus	brain
17	chr17:46018600-46019800	Active TSS	NHDF-Ad	bronchial
18	chr17:46018600-46020000	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr17:46018600-46020000	Active TSS	Esophagus	oesophagus
20	chr17:46018600-46020000	Active TSS	Fetal Kidney	kidney
21	chr17:46018600-46020200	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr17:46018600-46020200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:46018800-46019800	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr17:46018800-46019800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:46018800-46019800	Active TSS	Fetal Intestine Large	intestine
26	chr17:46018800-46019800	Bivalent/Poised TSS	HepG2	liver
27	chr17:46018800-46019800	Active TSS	HSMM	muscle
28	chr17:46018800-46020000	Active TSS	GM12878-XiMat	blood
29	chr17:46018800-46020400	Active TSS	HMEC	breast
30	chr17:46019000-46019800	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr17:46019000-46020000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr17:46019000-46020000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr17:46019200-46019800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr17:46019200-46019800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr17:46019200-46019800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr17:46019200-46019800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr17:46019200-46019800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr17:46019200-46019800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr17:46019200-46019800	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr17:46019200-46019800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr17:46019200-46019800	Flanking Active TSS	Placenta	Placenta
42	chr17:46019200-46019800	Flanking Active TSS	Thymus	Thymus
43	chr17:46019200-46020000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr17:46019200-46020000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr17:46019200-46020000	Flanking Active TSS	Fetal Brain Female	brain
46	chr17:46019200-46020000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr17:46019200-46020000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr17:46019200-46020000	Flanking Active TSS	HUVEC	blood vessel
49	chr17:46019200-46020000	Flanking Active TSS	NH-A	brain
50	chr17:46019200-46020200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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