Variant report

Variant	rs12475389
Chromosome Location	chr2:128265959-128265960
allele	C/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	MAX	chr2:128265709-128266800	A549	lung:	n/a	chr2:128266309-128266318
2	GATA3	chr2:128265851-128266846	A549	lung:	n/a	n/a
3	GATA3	chr2:128265822-128266863	SK-N-SH	brain:	n/a	n/a
4	KAP1	chr2:128265764-128266984	HEK293	kidney:	n/a	n/a
5	NFIC	chr2:128265886-128266889	SK-N-SH	brain:	n/a	n/a
6	CEBPB	chr2:128265937-128266735	HCT-116	colon:	n/a	n/a
7	FOSL2	chr2:128265544-128266763	A549	lung:	n/a	chr2:128266309-128266317 chr2:128266393-128266401 chr2:128266309-128266317 chr2:128266308-128266318 chr2:128266309-128266316
8	SP1	chr2:128265576-128266827	A549	lung:	n/a	n/a
9	JUND	chr2:128265931-128266716	SK-N-SH	brain:	n/a	chr2:128266309-128266317 chr2:128266393-128266401 chr2:128266309-128266317 chr2:128266308-128266318 chr2:128266309-128266316
10	TCF12	chr2:128265888-128266841	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr2:128265885-128266727	SK-N-SH	brain:	n/a	n/a
12	MXI1	chr2:128265736-128266846	IMR90	lung:	n/a	n/a
13	KAP1	chr2:128265777-128266796	U2OS	brain:	n/a	n/a
14	TCF12	chr2:128265872-128266764	A549	lung:	n/a	n/a
15	TCF7L2	chr2:128265884-128266564	Hela-S3	cervix:	n/a	chr2:128266198-128266207 chr2:128266196-128266206
16	FOS	chr2:128265830-128266648	MCF10A-Er-Src	breast:	n/a	chr2:128266309-128266317 chr2:128266393-128266401 chr2:128266309-128266317 chr2:128266308-128266318 chr2:128266309-128266316
17	EP300	chr2:128265928-128266762	SK-N-SH	brain:	n/a	chr2:128266309-128266318
18	GATA3	chr2:128265898-128266733	SK-N-SH	brain:	n/a	n/a
19	PBX3	chr2:128265941-128266762	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr2:128265847-128266110	ProgFib	skin:	n/a	n/a
21	FOSL1	chr2:128265867-128266692	HCT-116	colon:	n/a	chr2:128266309-128266317 chr2:128266393-128266401 chr2:128266309-128266317 chr2:128266308-128266318 chr2:128266309-128266316

No.	Distal block	Cell Line	Cell type
1	chr2:128261114..128269570-chr2:128281581..128286258,13	K562	blood:
2	chr2:128262614..128267545-chr2:128280339..128284643,6	K562	blood:
3	chr2:128255754..128258823-chr2:128264549..128267686,3	K562	blood:
4	chr2:128263369..128266760-chr2:128270837..128273303,3	K562	blood:
5	chr2:128262034..128264615-chr2:128264870..128267413,2	K562	blood:
6	chr2:128264079..128266201-chr2:128268340..128270505,2	MCF-7	breast:

Variant related genes	Relation type
IWS1	TF binding region
ENSG00000163166	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10432384	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10460269	0.83[AMR][1000 genomes]
rs10928770	0.83[AMR][1000 genomes]
rs11694581	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12463949	0.88[ASN][1000 genomes]
rs12466957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12475191	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12476558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13013022	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13026187	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13029611	0.81[ASN][1000 genomes]
rs1968396	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2052953	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2303947	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732207	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4507043	0.81[ASN][1000 genomes]
rs4662733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56398807	0.83[ASN][1000 genomes]
rs7583571	0.83[ASN][1000 genomes]
rs7590705	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128223600-128268800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:128235200-128270000	Strong transcription	Dnd41	blood
3	chr2:128239400-128266200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:128239400-128266400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:128246200-128271800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:128262600-128266000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:128262600-128283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:128263000-128266200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:128263000-128267600	Weak transcription	Stomach Mucosa	stomach
10	chr2:128263000-128272000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:128263000-128281200	Weak transcription	Fetal Kidney	kidney
12	chr2:128263200-128266200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:128263200-128266200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:128263200-128266400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr2:128263200-128267000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:128263200-128267400	Weak transcription	Primary B cells from cord blood	blood
17	chr2:128263200-128268600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:128263200-128268600	Weak transcription	Thymus	Thymus
19	chr2:128263200-128268800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:128263200-128269400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:128263200-128271400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:128263200-128271400	Weak transcription	Colonic Mucosa	Colon
23	chr2:128263200-128271600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:128263200-128271600	Weak transcription	Pancreas	Pancrea
25	chr2:128263200-128271600	Weak transcription	Spleen	Spleen
26	chr2:128263200-128271800	Weak transcription	Aorta	Aorta
27	chr2:128263200-128271800	Weak transcription	Brain Germinal Matrix	brain
28	chr2:128263200-128271800	Weak transcription	Esophagus	oesophagus
29	chr2:128263200-128282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:128263400-128266200	Weak transcription	Fetal Stomach	stomach
31	chr2:128263400-128268000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:128263400-128268600	Weak transcription	Fetal Thymus	thymus
33	chr2:128263400-128269600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:128263400-128271600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:128263400-128271600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:128263400-128271800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:128263400-128271800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:128263400-128275400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:128263600-128266200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr2:128263800-128266800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:128263800-128267800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:128263800-128269800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:128264200-128266600	Enhancers	Fetal Lung	lung
44	chr2:128264200-128266800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:128264200-128266800	Enhancers	NHEK	skin
46	chr2:128264200-128267000	Enhancers	Brain Substantia Nigra	brain
47	chr2:128264200-128267200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:128264200-128267200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:128264200-128267400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr2:128264200-128268200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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