Variant report

Variant	rs9596542
Chromosome Location	chr13:52165532-52165533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:142)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:142 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr13:52165280-52165550	HMEC	breast:	n/a	n/a
2	BCL3	chr13:52164980-52165671	A549	lung:	n/a	n/a
3	STAT5A	chr13:52164988-52165589	K562	blood:	n/a	n/a
4	FOSL2	chr13:52164917-52165804	SK-N-SH	brain:	n/a	n/a
5	MAX	chr13:52164881-52165620	A549	lung:	n/a	n/a
6	EP300	chr13:52164866-52165747	A549	lung:	n/a	chr13:52164900-52164914 chr13:52165092-52165105
7	RXRA	chr13:52164831-52165746	SK-N-SH	brain:	n/a	n/a
8	ATF3	chr13:52165001-52165539	K562	blood:	n/a	n/a
9	GATA1	chr13:52164852-52165915	PBDE	blood:	n/a	chr13:52165291-52165308
10	CEBPD	chr13:52165060-52165630	K562	blood:	n/a	n/a
11	SMARCB1	chr13:52164972-52165897	K562	blood:	n/a	n/a
12	MAX	chr13:52165067-52165639	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr13:52164975-52165619	SK-N-SH	brain:	n/a	n/a
14	FOXA1	chr13:52165274-52165612	T-47D	breast:	n/a	n/a
15	RAD21	chr13:52165318-52165542	GM12878	blood:	n/a	n/a
16	MAX	chr13:52165117-52165614	K562	blood:	n/a	n/a
17	BHLHE40	chr13:52165139-52165689	K562	blood:	n/a	n/a
18	USF2	chr13:52165148-52165666	Hela-S3	cervix:	n/a	n/a
19	GATA3	chr13:52164866-52165971	SK-N-SH	brain:	n/a	chr13:52165291-52165308
20	RAD21	chr13:52165140-52165665	HCT-116	colon:	n/a	n/a
21	PBX3	chr13:52164925-52165912	SK-N-SH	brain:	n/a	n/a
22	GATA2	chr13:52164988-52165588	K562	blood:	n/a	chr13:52165291-52165308
23	CEBPB	chr13:52165043-52165724	MCF-7	breast:	n/a	n/a
24	JUND	chr13:52164907-52165848	SK-N-SH	brain:	n/a	n/a
25	EP300	chr13:52165042-52165648	SK-N-SH_RA	brain:	n/a	chr13:52165092-52165105
26	MAX	chr13:52165101-52165619	NB4	blood:	n/a	n/a
27	EP300	chr13:52165184-52165795	T-47D	breast:	n/a	n/a
28	PML	chr13:52164970-52165612	K562	blood:	n/a	n/a
29	ZNF217	chr13:52165140-52165714	MCF-7	breast:	n/a	n/a
30	CCNT2	chr13:52165109-52165871	K562	blood:	n/a	n/a
31	CREB1	chr13:52164990-52165602	K562	blood:	n/a	n/a
32	NFIC	chr13:52164822-52165884	SK-N-SH	brain:	n/a	n/a
33	PML	chr13:52165016-52165566	K562	blood:	n/a	n/a
34	RAD21	chr13:52165018-52165643	Hela-S3	cervix:	n/a	n/a
35	GATA3	chr13:52164928-52165853	A549	lung:	n/a	chr13:52165291-52165308
36	CTCF	chr13:52165332-52165539	HUVEC	blood vessel:	n/a	n/a
37	RAD21	chr13:52165041-52165682	SK-N-SH_RA	brain:	n/a	n/a
38	FOXA2	chr13:52165128-52165617	A549	lung:	n/a	n/a
39	MAX	chr13:52165000-52165662	SK-N-SH	brain:	n/a	n/a
40	STAT3	chr13:52165063-52165545	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr13:52165095-52165573	K562	blood:	n/a	n/a
42	GATA2	chr13:52165081-52165592	K562	blood:	n/a	chr13:52165291-52165308
43	ATF1	chr13:52165081-52165823	K562	blood:	n/a	n/a
44	MYC	chr13:52165046-52165577	NB4	blood:	n/a	n/a
45	CEBPB	chr13:52164756-52165593	IMR90	lung:	n/a	n/a
46	ZBTB33	chr13:52165062-52165632	SK-N-SH	brain:	n/a	n/a
47	TEAD4	chr13:52165000-52165810	SK-N-SH	brain:	n/a	n/a
48	CTCF	chr13:52165400-52165550	BJ	skin:	n/a	n/a
49	CEBPB	chr13:52164875-52165739	A549	lung:	n/a	n/a
50	RAD21	chr13:52163760-52166017	SK-N-SH	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:52165459..52167828-chr13:52169558..52171705,2	K562	blood:
2	chr13:52015950..52029988-chr13:52150583..52166755,85	MCF-7	breast:
3	chr13:52022285..52029211-chr13:52148229..52167071,88	MCF-7	breast:
4	chr13:52163928..52166690-chr13:52169600..52171237,2	MCF-7	breast:
5	chr13:52165298..52167854-chr13:52172353..52174094,2	K562	blood:
6	chr13:52157062..52162024-chr13:52162079..52168293,13	MCF-7	breast:
7	chr13:52158311..52160568-chr13:52160634..52165811,6	MCF-7	breast:
8	chr13:52023783..52027256-chr13:52163004..52167854,10	K562	blood:
9	chr13:52025295..52029108-chr13:52160696..52165765,10	K562	blood:

No data

Variant related genes	Relation type
RNY1P6	TF binding region
ENSG00000224451	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000206920	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000224892	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10467509	1.00[AMR][1000 genomes]
rs9316549	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9316554	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9591413	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9596540	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9596546	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9596560	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52159600-52170600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:52159600-52174600	Weak transcription	Spleen	Spleen
3	chr13:52160200-52166000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:52160200-52166600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr13:52160200-52168000	Weak transcription	Pancreas	Pancrea
6	chr13:52160200-52170800	Weak transcription	Fetal Intestine Small	intestine
7	chr13:52160200-52181400	Weak transcription	Thymus	Thymus
8	chr13:52160400-52165600	Weak transcription	Colon Smooth Muscle	Colon
9	chr13:52160400-52173400	Weak transcription	Right Atrium	heart
10	chr13:52160400-52177000	Weak transcription	Right Ventricle	heart
11	chr13:52160600-52165600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr13:52160600-52169400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr13:52160600-52172200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr13:52160800-52166000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr13:52160800-52166200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr13:52160800-52166200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr13:52160800-52168000	Weak transcription	Primary T cells from cord blood	blood
18	chr13:52161200-52165800	Enhancers	Brain Substantia Nigra	brain
19	chr13:52161400-52165600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr13:52161400-52167000	Weak transcription	Primary B cells from cord blood	blood
21	chr13:52161400-52167600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr13:52161400-52168800	Weak transcription	Fetal Brain Female	brain
23	chr13:52161600-52166200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr13:52161800-52165800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr13:52161800-52166000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr13:52161800-52166000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr13:52161800-52166000	Enhancers	HepG2	liver
28	chr13:52161800-52166000	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr13:52162000-52165600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:52162000-52166200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr13:52162200-52166000	Enhancers	Adipose Nuclei	Adipose
32	chr13:52162200-52166000	Enhancers	Brain Hippocampus Middle	brain
33	chr13:52162200-52166200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr13:52162200-52166200	Enhancers	Brain Anterior Caudate	brain
35	chr13:52162800-52165600	Enhancers	HSMM	muscle
36	chr13:52162800-52166000	Enhancers	Brain Angular Gyrus	brain
37	chr13:52162800-52180200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr13:52163000-52166000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr13:52163000-52166200	Enhancers	Primary hematopoietic stem cells	blood
40	chr13:52163000-52166400	Enhancers	Hela-S3	cervix
41	chr13:52163000-52170400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr13:52163200-52182600	Weak transcription	Ovary	ovary
43	chr13:52163400-52166000	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr13:52163600-52166000	Enhancers	Brain Cingulate Gyrus	brain
45	chr13:52163600-52166200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr13:52163600-52166400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr13:52163800-52165800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr13:52163800-52166200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr13:52164000-52165800	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr13:52164000-52166000	Enhancers	HUVEC	blood vessel

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