Variant report

Variant	rs3756087
Chromosome Location	chr4:100871931-100871932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:355)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:355 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:100871118-100872085	SK-N-SH	brain:	n/a	n/a
2	REST	chr4:100869811-100872485	H1-neurons	neurons:	n/a	n/a
3	USF1	chr4:100871331-100872034	A549	lung:	n/a	n/a
4	MAZ	chr4:100871133-100872184	HepG2	liver:	n/a	chr4:100871615-100871624
5	POLR2A	chr4:100870314-100872085	GM10847	blood:	n/a	n/a
6	ZBTB7A	chr4:100871538-100872092	ECC-1	luminal epithelium:	n/a	chr4:100871979-100871988
7	EP300	chr4:100871822-100872024	HepG2	liver:	n/a	chr4:100871848-100871857
8	USF2	chr4:100871267-100872005	H1-hESC	embryonic stem cell:	n/a	chr4:100871735-100871746
9	CHD1	chr4:100869993-100872188	GM12878	blood:	n/a	n/a
10	REST	chr4:100870098-100872122	HL-60	blood:	n/a	n/a
11	CREB1	chr4:100871062-100872088	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr4:100870217-100872164	MCF-7	breast:	n/a	n/a
13	GTF2B	chr4:100871244-100872044	K562	blood:	n/a	n/a
14	BHLHE40	chr4:100871211-100872296	HepG2	liver:	n/a	n/a
15	TCF7L2	chr4:100871371-100871999	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr4:100870127-100872617	Raji	blood:	n/a	n/a
17	HA-E2F1	chr4:100870132-100872374	MCF-7	breast:	n/a	chr4:100871550-100871559
18	WRNIP1	chr4:100871195-100872513	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:100870146-100872114	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr4:100871594-100872036	A549	lung:	n/a	n/a
21	TBP	chr4:100870033-100872440	K562	blood:	n/a	n/a
22	MXI1	chr4:100871213-100872115	K562	blood:	n/a	n/a
23	MAX	chr4:100871098-100872287	ECC-1	luminal epithelium:	n/a	chr4:100871615-100871624
24	TCF7L2	chr4:100870151-100872183	HCT-116	colon:	n/a	n/a
25	MAX	chr4:100871207-100871973	A549	lung:	n/a	chr4:100871615-100871624
26	USF2	chr4:100871255-100871938	K562	blood:	n/a	chr4:100871735-100871746
27	USF1	chr4:100871523-100872006	A549	lung:	n/a	n/a
28	ZNF143	chr4:100870121-100872320	K562	blood:	n/a	chr4:100871616-100871634
29	ATF2	chr4:100871090-100872118	GM12878	blood:	n/a	n/a
30	ELF1	chr4:100871728-100872121	K562	blood:	n/a	n/a
31	CEBPB	chr4:100871252-100872560	Hela-S3	cervix:	n/a	chr4:100871551-100871559
32	POLR2A	chr4:100870150-100872017	HUVEC	blood vessel:	n/a	n/a
33	YY1	chr4:100871099-100872032	GM12878	blood:	n/a	chr4:100871848-100871857
34	MXI1	chr4:100871221-100872086	Hela-S3	cervix:	n/a	n/a
35	E2F4	chr4:100870192-100872121	K562	blood:	n/a	chr4:100871435-100871446 chr4:100870611-100870619 chr4:100870840-100870848 chr4:100871550-100871559
36	GATA2	chr4:100871159-100872048	SH-SY5Y	brain:	n/a	n/a
37	CHD2	chr4:100870041-100872130	K562	blood:	n/a	n/a
38	E2F4	chr4:100870128-100872613	MCF10A-Er-Src	breast:	n/a	chr4:100871435-100871446 chr4:100870611-100870619 chr4:100870840-100870848 chr4:100871550-100871559
39	TAF1	chr4:100870578-100871949	K562	blood:	n/a	n/a
40	YY1	chr4:100871072-100872118	HepG2	liver:	n/a	chr4:100871848-100871857
41	POLR2A	chr4:100871114-100872060	HepG2	liver:	n/a	n/a
42	POLR2A	chr4:100871187-100872071	HepG2	liver:	n/a	n/a
43	POLR2A	chr4:100871054-100872083	GM12892	blood:	n/a	n/a
44	TAF1	chr4:100871581-100872041	HepG2	liver:	n/a	n/a
45	MAX	chr4:100870079-100872227	ECC-1	luminal epithelium:	n/a	chr4:100871615-100871624
46	REST	chr4:100871140-100871948	HepG2	liver:	n/a	n/a
47	MAX	chr4:100871088-100872206	H1-hESC	embryonic stem cell:	n/a	chr4:100871615-100871624
48	MAX	chr4:100871252-100872102	K562	blood:	n/a	chr4:100871615-100871624
49	YY1	chr4:100871071-100871956	GM12878	blood:	n/a	chr4:100871848-100871857
50	USF2	chr4:100871434-100872177	GM12878	blood:	n/a	chr4:100871735-100871746

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:100799869..100822436-chr4:100866015..100873106,54	K562	blood:
2	chr4:99850379..99851880-chr4:100869996..100872136,2	K562	blood:
3	chr4:99848589..99851336-chr4:100870396..100872880,2	MCF-7	breast:
4	chr4:100814600..100817376-chr4:100869817..100872742,4	MCF-7	breast:
5	chr4:99848722..99851880-chr4:100870275..100872713,4	K562	blood:
6	chr4:100870088..100872119-chr4:103789876..103793001,3	K562	blood:
7	chr19:899198..902071-chr4:100869985..100872075,2	K562	blood:
8	chr4:100784573..100786604-chr4:100870218..100872169,2	K562	blood:
9	chr10:102825899..102826450-chr4:100871390..100872178,2	Hela-S3	cervix:
10	chr4:100871249..100872202-chr9:19230443..19231402,2	Hela-S3	cervix:
11	chr19:751070..751830-chr4:100870953..100871942,2	Hela-S3	cervix:
12	chr13:91999673..92001318-chr4:100870740..100872493,2	K562	blood:
13	chr4:99915655..99920524-chr4:100869895..100872849,4	K562	blood:
14	chr4:100870517..100873586-chr4:103747603..103750269,4	K562	blood:
15	chr4:100869383..100871934-chr4:102267599..102271042,3	K562	blood:
16	chr4:100737796..100739417-chr4:100869938..100872690,3	MCF-7	breast:
17	chr4:100810623..100827791-chr4:100865444..100874425,55	K562	blood:
18	chr4:100480938..100486909-chr4:100867873..100873651,15	K562	blood:
19	chr17:41465854..41466380-chr4:100871612..100872319,2	NB4	blood:
20	chr4:100871315..100874297-chr4:103746830..103749271,3	K562	blood:
21	chr4:100784573..100786137-chr4:100870218..100872755,2	K562	blood:
22	chr4:99915636..99917371-chr4:100869943..100872361,4	K562	blood:
23	chr4:100850716..100855335-chr4:100865818..100872882,15	K562	blood:
24	chr4:100824278..100827001-chr4:100871760..100873443,2	K562	blood:
25	chr17:79280417..79282564-chr4:100871183..100873116,2	MCF-7	breast:
26	chr4:100483475..100486481-chr4:100870338..100872441,3	MCF-7	breast:
27	chr4:100483327..100486538-chr4:100869980..100873651,6	K562	blood:
28	chr4:100840471..100849591-chr4:100866268..100873122,18	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DAPP1-2	chr4:100871517-100873711	NONHSAT097550
2	lnc-DAPP1-2	chr4:100871636-100873620	NR_002799

No data

Variant related genes	Relation type
DNAJB14	TF binding region
H2AFZ	TF binding region
ENSG00000138814	Chromatin interaction
ENSG00000107821	Chromatin interaction
ENSG00000164031	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000138823	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000137145	Chromatin interaction
ENSG00000145354	Chromatin interaction
ENSG00000254531	Chromatin interaction
ENSG00000109270	Chromatin interaction
ENSG00000246560	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000099812	Chromatin interaction
ENSG00000185168	Chromatin interaction
ENSG00000265213	Chromatin interaction
ENSG00000238449	Chromatin interaction
ENSG00000145331	Chromatin interaction
ENSG00000070190	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000263923	Chromatin interaction
ENSG00000198858	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10026048	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097676	0.95[JPT][hapmap]
rs11097677	0.95[JPT][hapmap]
rs11732776	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11935024	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11935399	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1365491	0.95[JPT][hapmap]
rs1365492	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs1365495	0.91[JPT][hapmap]
rs17029563	0.95[JPT][hapmap]
rs1863608	0.90[JPT][hapmap]
rs1896166	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1961323	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1972698	0.95[JPT][hapmap]
rs2070738	0.88[ASW][hapmap];0.89[CEU][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];0.83[AFR][1000 genomes]
rs2098937	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2114442	0.91[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2282588	0.91[JPT][hapmap]
rs2298735	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28404345	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2866174	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2866180	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28706589	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3775499	0.95[JPT][hapmap]
rs3775500	0.95[JPT][hapmap]
rs3775501	0.95[JPT][hapmap]
rs3775511	0.88[ASN][1000 genomes]
rs4699764	0.86[JPT][hapmap]
rs4699765	0.90[JPT][hapmap]
rs60978748	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532833	0.95[JPT][hapmap]
rs6532835	0.91[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6532836	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6811559	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6814895	0.95[JPT][hapmap]
rs6842840	0.88[ASW][hapmap];0.81[LWK][hapmap]
rs6848337	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6849599	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs6854536	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs715239	0.91[JPT][hapmap]
rs7675947	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7676564	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7684872	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7686428	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7689566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7692416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs919132	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs919133	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9307242	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][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	nsv879662	chr4:100849466-100876648	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
2	nsv879663	chr4:100866460-100876648	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
3	nsv967776	chr4:100869249-100872047	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
4	nsv822668	chr4:100869757-100872113	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv594944	chr4:100870899-100871931	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3756087	NFKB1	cis	cerebellum	SCAN
rs3756087	DAPP1	Cis_1M	lymphoblastoid	RTeQTL
rs3756087	MAPKSP1	cis	parietal	SCAN
rs3756087	MAPKSP1	cis	cerebellum	SCAN
rs3756087	NHEDC2	cis	cerebellum	SCAN
rs3756087	NHEDC1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100868600-100872200	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr4:100869000-100872400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:100869200-100872400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:100869200-100872800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:100869400-100872200	Active TSS	Brain Hippocampus Middle	brain
6	chr4:100869600-100872000	Active TSS	Fetal Brain Female	brain
7	chr4:100869600-100872200	Active TSS	NHLF	lung
8	chr4:100869600-100872400	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr4:100869600-100872400	Active TSS	NHDF-Ad	bronchial
10	chr4:100869800-100872000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr4:100869800-100872000	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr4:100869800-100872000	Active TSS	Thymus	Thymus
13	chr4:100869800-100872200	Active TSS	Fetal Intestine Small	intestine
14	chr4:100869800-100872400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:100869800-100872400	Active TSS	Fetal Intestine Large	intestine
16	chr4:100869800-100872600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr4:100869800-100872600	Active TSS	Stomach Smooth Muscle	stomach
18	chr4:100869800-100872600	Active TSS	HSMMtube	muscle
19	chr4:100870000-100872400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:100870000-100872400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:100870000-100872400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:100870000-100872400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:100870000-100872400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:100870000-100872400	Active TSS	Esophagus	oesophagus
25	chr4:100870000-100872400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr4:100870000-100872400	Active TSS	Ovary	ovary
27	chr4:100870000-100872400	Active TSS	Pancreas	Pancrea
28	chr4:100870000-100872600	Active TSS	Aorta	Aorta
29	chr4:100870000-100872600	Active TSS	Fetal Muscle Trunk	muscle
30	chr4:100870000-100872600	Active TSS	Left Ventricle	heart
31	chr4:100870000-100872600	Active TSS	Right Ventricle	heart
32	chr4:100870200-100872000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:100870200-100872000	Active TSS	Primary B cells from peripheral blood	blood
34	chr4:100870200-100872000	Active TSS	Primary T cells from cord blood	blood
35	chr4:100870200-100872000	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr4:100870200-100872000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:100870200-100872000	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr4:100870200-100872000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:100870200-100872000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr4:100870200-100872000	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr4:100870200-100872000	Active TSS	Fetal Brain Male	brain
42	chr4:100870200-100872000	Active TSS	Placenta	Placenta
43	chr4:100870200-100872000	Active TSS	HMEC	breast
44	chr4:100870200-100872000	Active TSS	HUVEC	blood vessel
45	chr4:100870200-100872000	Active TSS	NH-A	brain
46	chr4:100870200-100872200	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr4:100870200-100872200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:100870200-100872200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:100870200-100872200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:100870200-100872200	Active TSS	Primary T helper naive cells from peripheral blood	blood

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