Variant report

Variant	rs1000528
Chromosome Location	chr1:114471189-114471190
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	POLR2A	chr1:114470792-114473521	GM12878	blood:	n/a	n/a
2	IRF1	chr1:114470487-114471298	K562	blood:	n/a	n/a
3	IRF3	chr1:114470791-114471574	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:114470836-114473396	K562	blood:	n/a	n/a
5	STAT1	chr1:114471171-114471250	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:114471073-114473562	GM12878	blood:	n/a	n/a
7	MXI1	chr1:114470648-114473883	SK-N-SH	brain:	n/a	n/a
8	POU2F2	chr1:114470925-114471537	GM12878	blood:	n/a	chr1:114471312-114471325
9	MAFK	chr1:114470700-114472281	K562	blood:	n/a	n/a
10	CHD1	chr1:114471119-114472254	GM12878	blood:	n/a	chr1:114472166-114472176
11	GABPA	chr1:114470713-114473802	MCF-7	breast:	n/a	chr1:114472320-114472329
12	TBL1XR1	chr1:114470882-114472320	GM12878	blood:	n/a	n/a
13	FOXA1	chr1:114470686-114471214	HepG2	liver:	n/a	n/a
14	HEY1	chr1:114471146-114472447	HepG2	liver:	n/a	chr1:114472277-114472292
15	POLR2A	chr1:114470824-114473119	Raji	blood:	n/a	n/a
16	TBP	chr1:114470891-114473736	K562	blood:	n/a	n/a
17	RUNX3	chr1:114470721-114472371	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:114470968-114472954	HepG2	liver:	n/a	n/a
19	SPI1	chr1:114470931-114471386	HL-60	blood:	n/a	n/a
20	POLR2A	chr1:114470515-114473570	K562	blood:	n/a	n/a
21	TBP	chr1:114470932-114472285	GM12878	blood:	n/a	n/a
22	RELA	chr1:114470893-114472346	GM15510	blood:	n/a	n/a
23	RUNX3	chr1:114471057-114472354	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:114470779-114472422	GM12878	blood:	n/a	n/a
25	ZC3H11A	chr1:114471029-114472339	K562	blood:	n/a	n/a
26	SRF	chr1:114470588-114473873	MCF-7	breast:	n/a	chr1:114472196-114472206 chr1:114471150-114471165
27	YY1	chr1:114471176-114471535	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:114470886-114473746	MCF10A-Er-Src	breast:	n/a	n/a
29	BHLHE40	chr1:114471029-114473735	GM12878	blood:	n/a	chr1:114472288-114472304 chr1:114472299-114472315
30	POU2F2	chr1:114470927-114471517	GM12878	blood:	n/a	chr1:114471312-114471325
31	EBF1	chr1:114470769-114472303	GM12878	blood:	n/a	chr1:114471068-114471079
32	POLR2A	chr1:114471124-114471358	ProgFib	skin:	n/a	n/a
33	ELF1	chr1:114470758-114473795	MCF-7	breast:	n/a	chr1:114472196-114472208 chr1:114472308-114472320
34	POLR2A	chr1:114471120-114473277	GM12892	blood:	n/a	n/a
35	PML	chr1:114470862-114473466	GM12878	blood:	n/a	n/a
36	HCFC1	chr1:114470719-114473749	Hela-S3	cervix:	n/a	n/a
37	MAX	chr1:114470268-114473816	MCF-7	breast:	n/a	chr1:114472800-114472810 chr1:114473592-114473601
38	MYC	chr1:114470965-114473662	NB4	blood:	n/a	chr1:114472800-114472810 chr1:114473592-114473601
39	POU2F2	chr1:114471071-114471432	GM12891	blood:	n/a	chr1:114471312-114471325
40	ELF1	chr1:114470672-114473610	MCF-7	breast:	n/a	chr1:114472196-114472208 chr1:114472308-114472320
41	PML	chr1:114471106-114473468	MCF-7	breast:	n/a	n/a
42	CUX1	chr1:114470815-114471830	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:114471023-114473575	HL-60	blood:	n/a	n/a
44	POLR2A	chr1:114470811-114473054	GM19099	blood:	n/a	n/a
45	POLR2A	chr1:114470743-114474773	IMR90	lung:	n/a	n/a
46	MAX	chr1:114470698-114473363	MCF-7	breast:	n/a	chr1:114472800-114472810
47	CREB1	chr1:114471143-114472481	GM12878	blood:	n/a	n/a
48	SIN3A	chr1:114471045-114473584	GM12878	blood:	n/a	chr1:114472939-114472947 chr1:114472289-114472302
49	UBTF	chr1:114471176-114473691	K562	blood:	n/a	n/a
50	POLR2A	chr1:114470765-114472375	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:114471153..114473640-chr17:59476771..59478545,2	MCF-7	breast:
2	chr1:114377772..114378781-chr1:114470981..114471810,3	MCF-7	breast:
3	chr1:108289707..108293879-chr1:114470865..114473423,4	MCF-7	breast:
4	chr1:114447550..114448281-chr1:114470787..114471482,2	MCF-7	breast:
5	chr1:114353086..114356383-chr1:114467552..114475359,15	MCF-7	breast:
6	chr1:114299235..114302663-chr1:114470274..114473459,3	K562	blood:
7	chr1:114300069..114302951-chr1:114469985..114474355,4	MCF-7	breast:
8	chr1:114351760..114356326-chr1:114471041..114474785,9	K562	blood:
9	chr1:114444168..114452207-chr1:114466193..114476714,61	K562	blood:
10	chr1:114469554..114476691-chr1:114493097..114498363,7	MCF-7	breast:
11	chr1:114447178..114448996-chr1:114471115..114472973,22	MCF-7	breast:
12	chr1:114300200..114301915-chr1:114470901..114473894,2	MCF-7	breast:
13	chr1:108741161..108744200-chr1:114469971..114473274,3	MCF-7	breast:
14	chr1:114352160..114355349-chr1:114470537..114474785,4	K562	blood:
15	chr1:114470673..114473075-chr16:450178..453136,2	MCF-7	breast:
16	chr1:114439933..114443921-chr1:114470851..114474658,5	K562	blood:
17	chr1:114352067..114356642-chr1:114470131..114477025,16	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP4B1-1	chr1:114470866-114471854	ENSG00000235527

Variant related genes	Relation type
HIPK1	TF binding region
ENSG00000267280	Chromatin interaction
ENSG00000085491	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000242612	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000134215	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000260879	Chromatin interaction
ENSG00000134262	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1217441	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147079	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4381184	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs6658209	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6702833	0.87[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7522987	0.91[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs7545038	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551215	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7554371	0.87[EUR][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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription 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 target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1000528	NGF	cis	cerebellum	SCAN
rs1000528	OLFML3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114456200-114471200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:114470400-114471200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:114470400-114471200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:114470400-114471200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr1:114470400-114471400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:114470400-114471400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr1:114470400-114471600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:114470600-114471200	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr1:114470600-114471200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:114470600-114471200	Flanking Active TSS	K562	blood
11	chr1:114470600-114471400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr1:114470600-114471400	Active TSS	Stomach Smooth Muscle	stomach
13	chr1:114470600-114471600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:114470600-114471800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr1:114470800-114471200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:114470800-114471200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:114470800-114471200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr1:114470800-114471200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:114470800-114471200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:114470800-114471200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:114470800-114471200	Flanking Active TSS	Liver	Liver
22	chr1:114470800-114471200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:114470800-114471200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr1:114470800-114471200	Flanking Active TSS	Fetal Lung	lung
25	chr1:114470800-114471200	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr1:114470800-114471400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:114470800-114471400	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr1:114470800-114471400	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr1:114470800-114471400	Flanking Active TSS	Colon Smooth Muscle	Colon
30	chr1:114470800-114471400	Enhancers	Small Intestine	intestine
31	chr1:114470800-114471400	Flanking Active TSS	NHLF	lung
32	chr1:114470800-114471600	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr1:114470800-114471600	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr1:114470800-114471600	Active TSS	Fetal Brain Male	brain
35	chr1:114470800-114471600	Flanking Active TSS	Fetal Kidney	kidney
36	chr1:114470800-114471600	Flanking Active TSS	Fetal Stomach	stomach
37	chr1:114470800-114471600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr1:114470800-114471600	Flanking Active TSS	Rectal Smooth Muscle	rectum
39	chr1:114470800-114471600	Flanking Active TSS	NH-A	brain
40	chr1:114470800-114471600	Flanking Active TSS	NHEK	skin
41	chr1:114470800-114471600	Flanking Active TSS	Osteobl	bone
42	chr1:114470800-114471800	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr1:114470800-114471800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr1:114470800-114471800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:114470800-114471800	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr1:114470800-114471800	Flanking Active TSS	Hela-S3	cervix
47	chr1:114470800-114471800	Flanking Active TSS	HMEC	breast
48	chr1:114470800-114472000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:114470800-114472000	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr1:114470800-114473400	Active TSS	Fetal Intestine Large	intestine

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