Variant report

Variant	rs12428338
Chromosome Location	chr13:39591124-39591125
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	CTCF	chr13:39591060-39591210	GM12872	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
2	CTCF	chr13:39591060-39591210	Hela-S3	cervix:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
3	CTCF	chr13:39591080-39591230	HEEpiC	esophagus:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
4	CTCF	chr13:39590998-39591246	H1-hESC	embryonic stem cell:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
5	RAD21	chr13:39590945-39591200	SK-N-SH_RA	brain:	n/a	chr13:39591120-39591139 chr13:39591122-39591134 chr13:39591123-39591136
6	CTCF	chr13:39590997-39591243	K562	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
7	CTCF	chr13:39591000-39591150	HCM	heart:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
8	STAT3	chr13:39591013-39591412	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr13:39591040-39591190	SK-N-SH_RA	brain:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
10	CTCF	chr13:39591057-39591224	Pancreas_OC	pancreas:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
11	CTCF	chr13:39591040-39591190	GM12871	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
12	RAD21	chr13:39590828-39591337	MCF-7	breast:	n/a	chr13:39591120-39591139 chr13:39591122-39591134 chr13:39591123-39591136
13	CTCF	chr13:39590711-39591376	GM12878	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
14	CTCF	chr13:39591019-39591189	HepG2	liver:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
15	CTCF	chr13:39591023-39591205	GM12892	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
16	CTCF	chr13:39591021-39591216	GM19240	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
17	CTCF	chr13:39590980-39591130	GM12875	blood:	n/a	n/a
18	CTCF	chr13:39591027-39591237	Medullo	brain:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
19	CTCF	chr13:39590847-39591417	HCT-116	colon:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
20	CTCF	chr13:39591040-39591190	HepG2	liver:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
21	CTCF	chr13:39591029-39591197	MCF-7	breast:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
22	RAD21	chr13:39590883-39591338	HepG2	liver:	n/a	chr13:39591120-39591139 chr13:39591122-39591134 chr13:39591123-39591136
23	CTCF	chr13:39591040-39591190	HCM	heart:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
24	CTCF	chr13:39591028-39591270	LNCaP	prostate:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
25	CTCF	chr13:39591040-39591190	BE2_C	brain:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
26	CTCF	chr13:39591020-39591170	WERI-Rb-1	eye:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
27	CTCF	chr13:39591080-39591230	GM12872	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
28	CTCF	chr13:39591003-39591225	HepG2	liver:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
29	CTCF	chr13:39591020-39591170	HPF	lung:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
30	CTCF	chr13:39591060-39591210	NHLF	lung:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
31	CTCF	chr13:39590957-39591237	K562	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
32	CTCF	chr13:39591080-39591230	NB4	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
33	CTCF	chr13:39591020-39591170	GM12878	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
34	CTCF	chr13:39590976-39591251	MCF-7	breast:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
35	CTCF	chr13:39591040-39591190	GM12870	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
36	CTCF	chr13:39590988-39591232	Gliobla	brain:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
37	SMC3	chr13:39590966-39591283	Hela-S3	cervix:	n/a	chr13:39591124-39591138
38	CTCF	chr13:39591040-39591190	GM12875	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
39	POLR2A	chr13:39590428-39591631	K562	blood:	n/a	n/a
40	RAD21	chr13:39590871-39591249	H1-hESC	embryonic stem cell:	n/a	chr13:39591120-39591139 chr13:39591122-39591134 chr13:39591123-39591136
41	CTCF	chr13:39591080-39591230	AG10803	skin:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
42	CTCF	chr13:39591060-39591210	BJ	skin:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
43	CTCF	chr13:39591040-39591190	HPF	lung:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
44	CTCF	chr13:39591040-39591190	GM12874	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
45	RAD21	chr13:39590938-39591297	HepG2	liver:	n/a	chr13:39591120-39591139 chr13:39591122-39591134 chr13:39591123-39591136
46	RAD21	chr13:39590888-39591347	ECC-1	luminal epithelium:	n/a	chr13:39591120-39591139 chr13:39591122-39591134 chr13:39591123-39591136
47	CTCF	chr13:39591011-39591265	GM13977	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
48	CTCF	chr13:39591016-39591215	Fibrobl	skin:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
49	CTCF	chr13:39591060-39591210	GM12864	blood:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137
50	CTCF	chr13:39591020-39591170	SAEC	small airway:	n/a	chr13:39591117-39591138 chr13:39591122-39591140 chr13:39591124-39591137

No.	Distal block	Cell Line	Cell type
1	chr13:39588378..39591608-chr13:39610325..39612759,3	MCF-7	breast:
2	chr13:39581567..39584670-chr13:39588176..39591409,3	K562	blood:
3	chr13:39589682..39591724-chr13:39593267..39594841,2	K562	blood:

Variant related genes	Relation type
PROSER1	TF binding region
ENSG00000188811	Chromatin interaction
ENSG00000120685	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12428487	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12429615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12430798	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12431010	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12431083	1.00[AFR][1000 genomes]
rs12431327	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1575886	1.00[AFR][1000 genomes]
rs17226184	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17226219	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17226809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17235076	1.00[AFR][1000 genomes]
rs17235139	1.00[AFR][1000 genomes]
rs17826253	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs41286135	1.00[AFR][1000 genomes]
rs41286945	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39581600-39592000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr13:39581600-39592400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr13:39581800-39592200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:39581800-39593200	Strong transcription	HSMM	muscle
5	chr13:39581800-39597000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr13:39582000-39596600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr13:39582000-39608200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:39582200-39592600	Strong transcription	Fetal Thymus	thymus
9	chr13:39582200-39593400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr13:39582200-39596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr13:39582200-39596800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr13:39582200-39597400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr13:39582400-39605400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr13:39582600-39592000	Strong transcription	Placenta	Placenta
15	chr13:39582600-39592400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr13:39582600-39592400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr13:39582800-39593600	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr13:39583000-39592400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:39583200-39592400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr13:39583200-39592400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr13:39583200-39592400	Strong transcription	Adipose Nuclei	Adipose
22	chr13:39583200-39593200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr13:39583200-39606600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr13:39583400-39592400	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr13:39583400-39592600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:39583400-39593200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr13:39583600-39597200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr13:39583800-39592400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:39583800-39592600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr13:39584000-39597600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr13:39584200-39591200	Strong transcription	NHLF	lung
32	chr13:39584200-39591400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr13:39584200-39592400	Strong transcription	Osteobl	bone
34	chr13:39584400-39591400	Strong transcription	Primary hematopoietic stem cells	blood
35	chr13:39584400-39592400	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr13:39584400-39592400	Strong transcription	Dnd41	blood
37	chr13:39584400-39592600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr13:39584400-39593000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr13:39584400-39593200	Strong transcription	Fetal Kidney	kidney
40	chr13:39584600-39591400	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr13:39584600-39591400	Strong transcription	HMEC	breast
42	chr13:39584600-39591600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr13:39584600-39592400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr13:39584600-39592400	Strong transcription	Left Ventricle	heart
45	chr13:39584600-39592600	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr13:39584600-39592600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr13:39584600-39592600	Strong transcription	Fetal Muscle Leg	muscle
48	chr13:39584600-39592600	Strong transcription	HUVEC	blood vessel
49	chr13:39584600-39597600	Weak transcription	Fetal Heart	heart
50	chr13:39584600-39603600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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