Variant report

Variant	rs4411944
Chromosome Location	chr4:88340586-88340587
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	REST	chr4:88340471-88341155	PFSK-1	brain:	n/a	n/a
2	CEBPB	chr4:88340564-88341098	MCF-7	breast:	n/a	n/a
3	MYBL2	chr4:88340548-88341440	HepG2	liver:	n/a	n/a
4	MBD4	chr4:88340538-88341166	HepG2	liver:	n/a	n/a
5	FOXA1	chr4:88340521-88341390	HepG2	liver:	n/a	chr4:88340872-88340887 chr4:88340874-88340886
6	HDAC2	chr4:88340524-88341333	MCF-7	breast:	n/a	chr4:88341238-88341252
7	FOSL2	chr4:88340483-88341322	A549	lung:	n/a	chr4:88340917-88340927 chr4:88340915-88340926
8	HNF4A	chr4:88340571-88341197	HepG2	liver:	n/a	chr4:88341011-88341025 chr4:88341011-88341026 chr4:88341011-88341024 chr4:88340932-88340947 chr4:88340932-88340947 chr4:88341012-88341025 chr4:88341011-88341026 chr4:88341012-88341024
9	GATA3	chr4:88340315-88341503	MCF-7	breast:	n/a	n/a
10	MAFK	chr4:88340339-88341278	HepG2	liver:	n/a	n/a
11	NR3C1	chr4:88340560-88340988	A549	lung:	n/a	n/a
12	SP1	chr4:88340472-88341391	A549	lung:	n/a	n/a
13	TCF12	chr4:88340415-88341417	MCF-7	breast:	n/a	chr4:88340755-88340764
14	SP1	chr4:88340541-88341287	HepG2	liver:	n/a	n/a
15	ZNF217	chr4:88340378-88341204	MCF-7	breast:	n/a	n/a
16	HDAC2	chr4:88340489-88341209	HepG2	liver:	n/a	n/a
17	TCF12	chr4:88340583-88341050	A549	lung:	n/a	chr4:88340755-88340764
18	HDAC2	chr4:88340471-88341258	HepG2	liver:	n/a	chr4:88341238-88341252
19	EP300	chr4:88340390-88341191	A549	lung:	n/a	chr4:88340877-88340887
20	MYBL2	chr4:88340505-88341446	HepG2	liver:	n/a	n/a
21	FOXA1	chr4:88340477-88341336	HepG2	liver:	n/a	chr4:88340872-88340887 chr4:88340874-88340886
22	MAX	chr4:88340585-88341174	MCF-7	breast:	n/a	n/a
23	SP1	chr4:88340515-88341191	A549	lung:	n/a	n/a
24	NR3C1	chr4:88340576-88341161	A549	lung:	n/a	n/a
25	FOXA1	chr4:88340501-88341381	HepG2	liver:	n/a	chr4:88340872-88340887 chr4:88340874-88340886
26	HDAC2	chr4:88340509-88341225	MCF-7	breast:	n/a	n/a
27	TCF12	chr4:88340585-88341047	HepG2	liver:	n/a	chr4:88340755-88340764
28	EP300	chr4:88340471-88341109	A549	lung:	n/a	chr4:88340877-88340887
29	FOSL2	chr4:88340509-88341180	MCF-7	breast:	n/a	chr4:88340917-88340927 chr4:88340915-88340926
30	FOXA2	chr4:88340274-88341572	HepG2	liver:	n/a	chr4:88340874-88340886
31	NR2F2	chr4:88340458-88341391	MCF-7	breast:	n/a	n/a
32	TEAD4	chr4:88340368-88341346	HepG2	liver:	n/a	n/a
33	KAP1	chr4:88340554-88341529	HEK293	kidney:	n/a	n/a
34	GATA3	chr4:88340543-88341352	A549	lung:	n/a	n/a
35	REST	chr4:88340500-88341286	A549	lung:	n/a	n/a
36	FOXA2	chr4:88340499-88341169	A549	lung:	n/a	chr4:88340874-88340886
37	EP300	chr4:88340517-88341252	HepG2	liver:	n/a	chr4:88340877-88340887
38	GATA3	chr4:88340452-88341567	MCF-7	breast:	n/a	n/a
39	HNF4G	chr4:88340570-88341165	HepG2	liver:	n/a	chr4:88341011-88341025 chr4:88341011-88341026 chr4:88341011-88341024 chr4:88340932-88340947 chr4:88340932-88340947 chr4:88341012-88341025 chr4:88341011-88341026 chr4:88341012-88341024
40	NR3C1	chr4:88340538-88341160	A549	lung:	n/a	n/a
41	FOXA2	chr4:88340532-88341297	HepG2	liver:	n/a	chr4:88340874-88340886
42	POLR2A	chr4:88340357-88341470	PFSK-1	brain:	n/a	n/a
43	SIN3AK20	chr4:88340375-88341505	MCF-7	breast:	n/a	n/a
44	NFIC	chr4:88340555-88341310	HepG2	liver:	n/a	n/a
45	TCF7L2	chr4:88340438-88341704	PANC-1	pancreas:	n/a	n/a
46	FOXA1	chr4:88340506-88341331	HepG2	liver:	n/a	chr4:88340872-88340887 chr4:88340874-88340886
47	TCF12	chr4:88340344-88341590	A549	lung:	n/a	chr4:88340755-88340764
48	FOXA1	chr4:88340498-88341389	A549	lung:	n/a	chr4:88340872-88340887 chr4:88340874-88340886
49	NR2F2	chr4:88340519-88341399	HepG2	liver:	n/a	n/a
50	FOXA2	chr4:88340503-88341297	A549	lung:	n/a	chr4:88340874-88340886

No.	Distal block	Cell Line	Cell type
1	chr4:88340563..88342774-chr4:88344260..88346848,4	MCF-7	breast:
2	chr4:88339085..88341655-chr4:88342092..88343723,2	MCF-7	breast:
3	chr4:88339088..88340859-chr4:88343494..88345831,2	MCF-7	breast:

Variant related genes	Relation type
NUDT9	TF binding region
ENSG00000170502	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10000196	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10009948	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10023606	0.87[ASN][1000 genomes]
rs10024781	0.84[ASN][1000 genomes]
rs10030035	0.87[ASN][1000 genomes]
rs10032122	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10084883	0.87[ASN][1000 genomes]
rs12640451	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12640894	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12648665	0.85[EUR][1000 genomes]
rs12650763	0.87[ASN][1000 genomes]
rs12651034	0.87[ASN][1000 genomes]
rs28366407	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28415220	0.83[ASN][1000 genomes]
rs28437709	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28493315	0.87[ASN][1000 genomes]
rs28493566	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28529046	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28535549	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28712618	0.87[ASN][1000 genomes]
rs28718986	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28762371	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28805573	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34027531	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55824708	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56153912	0.87[ASN][1000 genomes]
rs58192677	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67121411	0.86[ASN][1000 genomes]
rs68045074	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72652067	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7665115	0.85[ASN][1000 genomes]
rs7673763	0.87[ASN][1000 genomes]
rs7677249	0.85[ASN][1000 genomes]
rs7680878	0.87[ASN][1000 genomes]
rs7690728	0.87[ASN][1000 genomes]
rs9995987	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9998212	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer 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	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88329600-88342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:88334600-88342800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:88336400-88340600	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr4:88337200-88340600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:88337400-88340600	Enhancers	Liver	Liver
6	chr4:88338400-88340600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:88339400-88343000	Enhancers	Fetal Intestine Large	intestine
8	chr4:88339800-88340600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:88340000-88343000	Enhancers	Fetal Intestine Small	intestine
10	chr4:88340000-88343000	Enhancers	Pancreas	Pancrea
11	chr4:88340400-88340800	Enhancers	A549	lung
12	chr4:88340400-88340800	Flanking Active TSS	HepG2	liver
13	chr4:88340400-88341400	Weak transcription	Small Intestine	intestine
14	chr4:88340400-88341400	Enhancers	HUVEC	blood vessel
15	chr4:88340400-88342000	Enhancers	Stomach Mucosa	stomach
16	chr4:88340400-88343000	Enhancers	Duodenum Mucosa	Duodenum

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