Variant report

Variant	rs238527
Chromosome Location	chr12:58129660-58129661
allele	G/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	RAD21	chr12:58129649-58130001	IMR90	lung:	n/a	chr12:58129957-58129969 chr12:58129822-58129836
2	RAD21	chr12:58129567-58129965	SK-N-SH_RA	brain:	n/a	chr12:58129822-58129836
3	CTCF	chr12:58129579-58130018	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr12:58129568-58130016	MCF-7	breast:	n/a	n/a
5	CTCF	chr12:58129637-58130000	K562	blood:	n/a	n/a
6	ZNF263	chr12:58128487-58130012	HEK293-T-REx	kidney:	n/a	chr12:58129279-58129288 chr12:58129602-58129611 chr12:58129566-58129575
7	RCOR1	chr12:58129312-58130607	K562	blood:	n/a	n/a
8	CTCF	chr12:58129618-58130117	K562	blood:	n/a	n/a
9	SIN3A	chr12:58129343-58130824	H1-hESC	embryonic stem cell:	n/a	chr12:58130201-58130214
10	RAD21	chr12:58129626-58130017	H1-hESC	embryonic stem cell:	n/a	chr12:58129957-58129969 chr12:58129822-58129836
11	TEAD4	chr12:58129612-58130054	K562	blood:	n/a	n/a
12	TBP	chr12:58129621-58130116	K562	blood:	n/a	n/a
13	SP1	chr12:58129563-58130127	H1-hESC	embryonic stem cell:	n/a	chr12:58130102-58130111
14	BCL3	chr12:58129418-58130018	A549	lung:	n/a	chr12:58129677-58129686 chr12:58130004-58130013
15	ZBTB7A	chr12:58129624-58130046	K562	blood:	n/a	n/a
16	RCOR1	chr12:58129548-58130062	K562	blood:	n/a	n/a
17	CTBP2	chr12:58129316-58131871	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr12:58129590-58130032	K562	blood:	n/a	n/a
19	CTCF	chr12:58129660-58129810	NHDF-neo	bronchial:	n/a	n/a
20	RAD21	chr12:58129602-58129978	HepG2	liver:	n/a	chr12:58129957-58129969 chr12:58129822-58129836
21	CTCF	chr12:58129476-58130102	MCF-7	breast:	n/a	n/a
22	CTCF	chr12:58129398-58130509	A549	lung:	n/a	chr12:58130211-58130220
23	MYC	chr12:58129654-58130447	K562	blood:	n/a	n/a
24	CTCF	chr12:58129640-58129790	HRPEpiC	eye:	n/a	n/a
25	CTCF	chr12:58129603-58129978	HepG2	liver:	n/a	n/a
26	RAD21	chr12:58129555-58130102	MCF-7	breast:	n/a	chr12:58129957-58129969 chr12:58129822-58129836
27	SMC3	chr12:58129655-58130002	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr12:58129659-58130009	IMR90	lung:	n/a	n/a
29	TCF12	chr12:58129582-58130741	A549	lung:	n/a	chr12:58130440-58130450
30	CTCF	chr12:58129640-58129790	HCM	heart:	n/a	n/a
31	MAX	chr12:58129600-58130719	A549	lung:	n/a	n/a
32	YY1	chr12:58129398-58130065	H1-hESC	embryonic stem cell:	n/a	n/a
33	ZNF143	chr12:58129597-58129990	H1-hESC	embryonic stem cell:	n/a	chr12:58129888-58129898
34	CTCF	chr12:58129619-58130004	K562	blood:	n/a	n/a
35	RAD21	chr12:58129655-58130052	A549	lung:	n/a	chr12:58129957-58129969 chr12:58129822-58129836
36	ATF2	chr12:58129579-58129960	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAZ	chr12:58129580-58131361	IMR90	lung:	n/a	n/a
38	HA-E2F1	chr12:58129591-58130197	MCF-7	breast:	n/a	chr12:58129888-58129898
39	MAZ	chr12:58129463-58130069	Hela-S3	cervix:	n/a	n/a
40	RAD21	chr12:58129518-58130092	A549	lung:	n/a	chr12:58129957-58129969 chr12:58129822-58129836
41	RAD21	chr12:58129561-58130063	ECC-1	luminal epithelium:	n/a	chr12:58129957-58129969 chr12:58129822-58129836
42	EGR1	chr12:58129578-58130101	H1-hESC	embryonic stem cell:	n/a	chr12:58130000-58130013 chr12:58129888-58129901 chr12:58130018-58130031
43	RAD21	chr12:58129585-58130065	HepG2	liver:	n/a	chr12:58129957-58129969 chr12:58129822-58129836
44	CTCF	chr12:58129650-58129986	HepG2	liver:	n/a	n/a
45	ELF1	chr12:58129623-58129951	A549	lung:	n/a	n/a
46	MAZ	chr12:58129474-58130493	K562	blood:	n/a	n/a
47	RAD21	chr12:58129631-58129980	K562	blood:	n/a	chr12:58129957-58129969 chr12:58129822-58129836
48	CBX3	chr12:58129610-58130695	K562	blood:	n/a	n/a
49	MAZ	chr12:58129436-58129976	HepG2	liver:	n/a	n/a
50	RAD21	chr12:58129596-58130017	A549	lung:	n/a	chr12:58129957-58129969 chr12:58129822-58129836

No.	Distal block	Cell Line	Cell type
1	chr12:57856179..57858498-chr12:58127596..58129840,2	K562	blood:
2	chr12:57915857..57917548-chr12:58128281..58130652,2	MCF-7	breast:
3	chr12:57951614..57954558-chr12:58128271..58131020,2	K562	blood:
4	chr12:58129311..58130058-chr12:58298904..58299889,3	MCF-7	breast:
5	chr12:58086411..58090647-chr12:58128680..58131579,3	MCF-7	breast:
6	chr12:58016846..58018792-chr12:58129433..58131831,2	K562	blood:
7	chr12:58086094..58088041-chr12:58129129..58130888,2	K562	blood:
8	chr12:57985447..57987407-chr12:58128480..58131325,2	MCF-7	breast:
9	chr12:57934862..57937510-chr12:58129218..58130977,3	K562	blood:
10	chr12:58014906..58016961-chr12:58128240..58131170,2	K562	blood:
11	chr12:57914398..57918240-chr12:58127433..58131340,5	K562	blood:
12	chr12:57976905..57977643-chr12:58129262..58129943,2	MCF-7	breast:
13	chr12:58112503..58116669-chr12:58128862..58132734,4	K562	blood:
14	chr12:57856220..57856940-chr12:58129447..58130061,2	MCF-7	breast:
15	chr12:57976837..57977750-chr12:58129328..58130470,7	MCF-7	breast:
16	chr12:57934862..57936382-chr12:58129218..58130903,2	K562	blood:
17	chr12:58117957..58120676-chr12:58129042..58131410,3	K562	blood:
18	chr12:57976568..57977825-chr12:58129195..58130317,11	K562	blood:
19	chr12:57909973..57915898-chr12:58127755..58134567,15	K562	blood:

Variant related genes	Relation type
AGAP2	TF binding region
TSPAN31	TF binding region
ENSG00000111087	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000135502	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000257342	Chromatin interaction
ENSG00000166987	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs3211605	1.00[ASN][1000 genomes]
rs3211607	1.00[ASN][1000 genomes]
rs3211614	1.00[ASN][1000 genomes]
rs4447215	0.95[GIH][hapmap]
rs4760322	1.00[ASN][1000 genomes]
rs4760331	0.95[GIH][hapmap]
rs73338229	1.00[ASN][1000 genomes]
rs73338231	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8176339	1.00[ASN][1000 genomes]
rs8176346	1.00[ASN][1000 genomes]
rs8176350	0.95[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv1851618	chr12:58109302-58131947	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
7	nsv899122	chr12:58118248-58137563	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	esv3363572	chr12:58129335-58133633	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs238527	PHLPP1	trans	lymphoblastoid	seeQTL
rs238527	RHOB	trans	lymphoblastoid	seeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58118400-58132000	Strong transcription	Primary T cells from cord blood	blood
2	chr12:58119200-58132000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:58119600-58130400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:58119600-58130400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:58119600-58131200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr12:58119600-58131400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:58119600-58132400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:58119600-58132800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:58119600-58133000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:58120000-58131400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr12:58120200-58130200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:58120400-58131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:58120400-58132400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:58121400-58132800	Strong transcription	Thymus	Thymus
15	chr12:58121600-58130200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr12:58121800-58130200	Weak transcription	Gastric	stomach
17	chr12:58121800-58132400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:58123000-58131400	Strong transcription	Fetal Thymus	thymus
19	chr12:58127800-58133600	Weak transcription	GM12878-XiMat	blood
20	chr12:58128000-58131600	Bivalent Enhancer	Placenta	Placenta
21	chr12:58128200-58129800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:58128400-58130200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:58128600-58130400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr12:58128800-58130000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:58129000-58129800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:58129000-58130000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:58129000-58130400	Enhancers	Liver	Liver
28	chr12:58129000-58131600	Genic enhancers	Primary T cells fromperipheralblood	blood
29	chr12:58129000-58131600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
30	chr12:58129000-58131600	Bivalent Enhancer	Fetal Brain Male	brain
31	chr12:58129000-58131800	Bivalent Enhancer	Fetal Stomach	stomach
32	chr12:58129000-58132200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:58129000-58132400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr12:58129000-58132800	Weak transcription	Dnd41	blood
35	chr12:58129200-58130200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
36	chr12:58129200-58130600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:58129200-58131400	Bivalent Enhancer	Brain Substantia Nigra	brain
38	chr12:58129200-58131800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
39	chr12:58129200-58132600	Weak transcription	Primary B cells from cord blood	blood
40	chr12:58129200-58132600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr12:58129400-58129800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
42	chr12:58129400-58129800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:58129400-58129800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
44	chr12:58129400-58129800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
45	chr12:58129400-58129800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
46	chr12:58129400-58129800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:58129400-58129800	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr12:58129400-58129800	Bivalent Enhancer	Left Ventricle	heart
49	chr12:58129400-58129800	Flanking Active TSS	HSMMtube	muscle
50	chr12:58129400-58130000	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain

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