Variant report

Variant	rs12508481
Chromosome Location	chr4:95680361-95680362
allele	C/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	TAF1	chr4:95679975-95680391	PFSK-1	brain:	n/a	n/a
2	MXI1	chr4:95677488-95681982	SK-N-SH	brain:	n/a	chr4:95679721-95679730
3	MAX	chr4:95678600-95680454	A549	lung:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
4	HA-E2F1	chr4:95678701-95680381	MCF-7	breast:	n/a	chr4:95679542-95679552 chr4:95679544-95679553 chr4:95680197-95680204 chr4:95679618-95679630 chr4:95679539-95679549
5	SP1	chr4:95680026-95680605	A549	lung:	n/a	n/a
6	STAT3	chr4:95680329-95681426	MCF10A-Er-Src	breast:	n/a	chr4:95681017-95681028 chr4:95680706-95680714 chr4:95681019-95681027 chr4:95680965-95680973
7	SIN3AK20	chr4:95680058-95680422	PFSK-1	brain:	n/a	n/a
8	RAD21	chr4:95680004-95680456	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr4:95679628-95680442	PFSK-1	brain:	n/a	n/a
10	TCF12	chr4:95679460-95681991	A549	lung:	n/a	chr4:95679721-95679731
11	TAF1	chr4:95679876-95680431	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr4:95679598-95680542	A549	lung:	n/a	chr4:95679686-95679699
13	TAF1	chr4:95679397-95680588	A549	lung:	n/a	n/a
14	KAP1	chr4:95679949-95681335	HEK293	kidney:	n/a	n/a
15	FOSL2	chr4:95679587-95680387	A549	lung:	n/a	chr4:95679676-95679685 chr4:95680374-95680384
16	ZNF263	chr4:95679259-95680394	HEK293-T-REx	kidney:	n/a	n/a
17	CTCF	chr4:95680320-95680470	HEEpiC	esophagus:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:95679956..95681773-chr4:96032755..96034458,2	MCF-7	breast:
2	chr4:95679588..95681847-chr4:96013272..96015095,2	MCF-7	breast:
3	chr4:95679939..95682877-chr4:95683215..95684845,2	MCF-7	breast:
4	chr4:95679187..95680719-chr4:95971290..95974263,2	MCF-7	breast:
5	chr4:95678678..95680883-chr4:96023985..96026151,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249599	TF binding region
ENSG00000138696	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs34016280	0.93[ASN][1000 genomes]
rs34328418	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4348103	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4699361	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56214010	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62316512	0.82[AMR][1000 genomes];0.88[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	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1005816	chr4:95573444-95902704	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv3407255	chr4:95677954-95680802	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95677800-95681800	Active TSS	A549	lung
2	chr4:95678000-95682000	Active TSS	Stomach Smooth Muscle	stomach
3	chr4:95678200-95680400	Active TSS	Aorta	Aorta
4	chr4:95678200-95680400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
5	chr4:95678200-95680400	Active TSS	HMEC	breast
6	chr4:95678400-95680400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr4:95678400-95680600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
8	chr4:95678400-95680600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr4:95678400-95680600	Active TSS	Ovary	ovary
10	chr4:95678400-95680800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:95678400-95680800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr4:95678600-95680400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:95678600-95680400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:95678600-95680400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:95678600-95680400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
16	chr4:95678600-95680400	Active TSS	Brain Substantia Nigra	brain
17	chr4:95678600-95680400	Bivalent/Poised TSS	Fetal Stomach	stomach
18	chr4:95678600-95680400	Active TSS	Pancreas	Pancrea
19	chr4:95678600-95680600	Active TSS	Brain Anterior Caudate	brain
20	chr4:95678600-95680600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr4:95678600-95680600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
22	chr4:95678800-95680400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr4:95678800-95680400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr4:95678800-95680400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:95678800-95680600	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
26	chr4:95679000-95680400	Bivalent/Poised TSS	Osteobl	bone
27	chr4:95679000-95680600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr4:95679600-95680400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:95679600-95680400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr4:95679600-95680400	Flanking Bivalent TSS/Enh	Dnd41	blood
31	chr4:95679600-95680600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr4:95679600-95680600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr4:95679600-95680600	Bivalent/Poised TSS	Fetal Brain Female	brain
34	chr4:95679600-95680800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr4:95679600-95680800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
36	chr4:95679600-95681600	Bivalent/Poised TSS	Fetal Kidney	kidney
37	chr4:95679800-95680400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:95679800-95680400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr4:95679800-95680400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:95679800-95680400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
41	chr4:95679800-95680400	Enhancers	Spleen	Spleen
42	chr4:95679800-95680600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr4:95680000-95680400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:95680000-95680400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:95680000-95680400	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
46	chr4:95680000-95680400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:95680000-95680400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr4:95680000-95680400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
49	chr4:95680000-95680400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
50	chr4:95680000-95680400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet

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