Variant report

Variant	rs9288134
Chromosome Location	chr2:153573363-153573364
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	MBD4	chr2:153573120-153575962	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:153572495-153576612	MCF10A-Er-Src	breast:	n/a	n/a
3	SIN3A	chr2:153573139-153575943	H1-hESC	embryonic stem cell:	n/a	chr2:153574775-153574788
4	CTCF	chr2:153573260-153573410	NHLF	lung:	n/a	chr2:153573370-153573388
5	TAF1	chr2:153573339-153575837	ECC-1	luminal epithelium:	n/a	n/a
6	JUND	chr2:153573361-153575603	GM12878	blood:	n/a	chr2:153574146-153574155 chr2:153574147-153574156 chr2:153575007-153575021
7	PML	chr2:153573188-153576331	K562	blood:	n/a	n/a
8	POLR2A	chr2:153573348-153575507	H1-neurons	neurons:	n/a	n/a
9	SIN3AK20	chr2:153573318-153574425	H1-hESC	embryonic stem cell:	n/a	n/a
10	HEY1	chr2:153573173-153576234	K562	blood:	n/a	chr2:153575077-153575092 chr2:153575049-153575064
11	MYC	chr2:153572377-153574144	MCF10A-Er-Src	breast:	n/a	chr2:153573447-153573457
12	CTCF	chr2:153573240-153573390	BE2_C	brain:	n/a	chr2:153573370-153573388
13	POLR2A	chr2:153573256-153576290	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr2:153573363-153575781	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr2:153573260-153573410	HAc	cerebellar:	n/a	chr2:153573370-153573388
16	MAX	chr2:153573298-153575884	HepG2	liver:	n/a	chr2:153573447-153573457
17	TAF1	chr2:153573292-153575798	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAZ	chr2:153573347-153576076	K562	blood:	n/a	chr2:153573447-153573457
19	PML	chr2:153573249-153576154	GM12878	blood:	n/a	n/a
20	TAF1	chr2:153573343-153575498	H1-neurons	neurons:	n/a	n/a
21	MXI1	chr2:153573116-153575788	GM12878	blood:	n/a	chr2:153575089-153575098
22	HCFC1	chr2:153573358-153575813	K562	blood:	n/a	n/a
23	NFYB	chr2:153573360-153575748	K562	blood:	n/a	chr2:153575059-153575074 chr2:153575061-153575076
24	TBP	chr2:153573346-153576089	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr2:153573311-153575744	GM12891	blood:	n/a	n/a
26	MYC	chr2:153573340-153575808	K562	blood:	n/a	chr2:153573447-153573457
27	WRNIP1	chr2:153573280-153573940	GM12878	blood:	n/a	n/a
28	MXI1	chr2:153573070-153575705	IMR90	lung:	n/a	chr2:153575089-153575098
29	POLR2A	chr2:153573287-153577046	GM12878	blood:	n/a	n/a
30	EP300	chr2:153572956-153573369	GM12878	blood:	n/a	chr2:153573244-153573254
31	POLR2A	chr2:153572295-153576273	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr2:153573288-153576623	K562	blood:	n/a	n/a
33	CTCF	chr2:153573340-153573490	RPTEC	kidney:	n/a	chr2:153573370-153573388
34	SREBP1	chr2:153570771-153575432	GM12878	blood:	n/a	n/a
35	POLR2A	chr2:153573348-153576064	Raji	blood:	n/a	n/a
36	MXI1	chr2:153572226-153576757	SK-N-SH	brain:	n/a	chr2:153575089-153575098
37	POLR2A	chr2:153573350-153576074	Hela-S3	cervix:	n/a	n/a
38	RCOR1	chr2:153573334-153576069	K562	blood:	n/a	n/a
39	MAX	chr2:153573235-153575929	A549	lung:	n/a	chr2:153573447-153573457
40	BCL3	chr2:153573358-153574755	A549	lung:	n/a	n/a
41	POLR2A	chr2:153573255-153576130	GM12878	blood:	n/a	n/a
42	BHLHE40	chr2:153573252-153575753	K562	blood:	n/a	n/a
43	MYC	chr2:153573348-153575757	K562	blood:	n/a	chr2:153573447-153573457
44	STAT5A	chr2:153573302-153575658	GM12878	blood:	n/a	chr2:153574281-153574293 chr2:153573449-153573461 chr2:153574149-153574161 chr2:153573453-153573465 chr2:153574152-153574164 chr2:153574223-153574235 chr2:153574146-153574158
45	MAX	chr2:153573355-153575870	MCF-7	breast:	n/a	chr2:153573447-153573457
46	YY1	chr2:153572946-153573546	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:153573326-153575842	HL-60	blood:	n/a	n/a
48	POLR2A	chr2:153573323-153575758	GM12891	blood:	n/a	n/a
49	CTCF	chr2:153573079-153573451	K562	blood:	n/a	chr2:153573370-153573388
50	MAX	chr2:153573336-153575863	HepG2	liver:	n/a	chr2:153573447-153573457

No.	Distal block	Cell Line	Cell type
1	chr2:153572649..153576015-chr2:157196773..157199686,4	K562	blood:
2	chr2:153031056..153034207-chr2:153571978..153575897,4	K562	blood:
3	chr2:153573043..153575205-chr8:143832270..143834692,2	MCF-7	breast:
4	chr2:153030783..153033861-chr2:153572629..153575835,5	MCF-7	breast:

Variant related genes	Relation type
ARL6IP6	TF binding region
PRPF40A	TF binding region
ENSG00000153234	Chromatin interaction
ENSG00000197353	Chromatin interaction
ENSG00000115145	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10168450	0.91[AFR][1000 genomes]
rs10171860	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10181036	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs13389152	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16831583	1.00[CEU][hapmap]
rs16831742	1.00[CEU][hapmap]
rs16831745	1.00[CEU][hapmap]
rs6738344	0.95[YRI][hapmap]
rs7597046	1.00[CEU][hapmap];0.81[AFR][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	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 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	chr2:153558800-153573400	Weak transcription	Spleen	Spleen
2	chr2:153566800-153573400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:153571800-153573400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:153572000-153573800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:153572000-153576400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:153572000-153576400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:153572000-153576400	Active TSS	K562	blood
8	chr2:153572200-153576400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:153572200-153576400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:153572200-153576400	Active TSS	HMEC	breast
11	chr2:153572200-153576800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr2:153572200-153577000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr2:153572400-153573400	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr2:153572400-153573400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
15	chr2:153572400-153573400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr2:153572400-153573400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:153572400-153573400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:153572400-153573400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:153572400-153573400	Flanking Active TSS	Liver	Liver
20	chr2:153572400-153573400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr2:153572400-153573400	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr2:153572400-153573600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr2:153572400-153573600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:153572400-153573600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr2:153572400-153573600	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr2:153572400-153573600	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr2:153572400-153573600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr2:153572400-153573800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr2:153572400-153573800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr2:153572400-153573800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr2:153572400-153574400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
32	chr2:153572400-153575800	Active TSS	Fetal Brain Female	brain
33	chr2:153572400-153575800	Active TSS	Hela-S3	cervix
34	chr2:153572400-153576000	Active TSS	HSMM	muscle
35	chr2:153572400-153576200	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr2:153572400-153576200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:153572400-153576400	Active TSS	H1 Cell Line	embryonic stem cell
38	chr2:153572400-153576400	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr2:153572400-153576400	Active TSS	Fetal Kidney	kidney
40	chr2:153572400-153576400	Active TSS	A549	lung
41	chr2:153572400-153576600	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr2:153572400-153576600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:153572400-153576600	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr2:153572400-153576600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:153572400-153576600	Active TSS	NHLF	lung
46	chr2:153572400-153576800	Active TSS	H9 Cell Line	embryonic stem cell
47	chr2:153572400-153576800	Active TSS	Psoas Muscle	Psoas
48	chr2:153572400-153577000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:153572400-153577000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:153572600-153573400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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