Variant report

Variant	rs28360466
Chromosome Location	chr12:121647870-121647871
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	CCNT2	chr12:121647421-121648519	K562	blood:	n/a	n/a
2	TCF3	chr12:121647816-121648082	GM12878	blood:	n/a	n/a
3	RCOR1	chr12:121647596-121648930	K562	blood:	n/a	n/a
4	RAD21	chr12:121647519-121648108	A549	lung:	n/a	n/a
5	RAD21	chr12:121647627-121648020	SK-N-SH_RA	brain:	n/a	n/a
6	RAD21	chr12:121647706-121647999	Hela-S3	cervix:	n/a	n/a
7	HDAC2	chr12:121647594-121648341	HepG2	liver:	n/a	n/a
8	RCOR1	chr12:121647697-121648205	GM12878	blood:	n/a	n/a
9	GABPA	chr12:121647850-121648166	H1-hESC	embryonic stem cell:	n/a	chr12:121647953-121647962
10	TCF7L2	chr12:121647564-121648215	HCT-116	colon:	n/a	n/a
11	CHD2	chr12:121647843-121648167	HepG2	liver:	n/a	n/a
12	CTCF	chr12:121647628-121648031	K562	blood:	n/a	chr12:121647877-121647890
13	CTCF	chr12:121647820-121647970	SK-N-SH_RA	brain:	n/a	chr12:121647877-121647890
14	GTF2F1	chr12:121647720-121648121	K562	blood:	n/a	n/a
15	TAL1	chr12:121647754-121648201	K562	blood:	n/a	n/a
16	ELF1	chr12:121647673-121648065	A549	lung:	n/a	n/a
17	CTCF	chr12:121647720-121647870	K562	blood:	n/a	n/a
18	CTCF	chr12:121647820-121647970	HCM	heart:	n/a	chr12:121647877-121647890
19	MAX	chr12:121647747-121648466	MCF-7	breast:	n/a	chr12:121648179-121648190
20	CTCF	chr12:121647676-121648044	T-47D	breast:	n/a	chr12:121647877-121647890
21	CTCF	chr12:121647720-121647870	RPTEC	kidney:	n/a	n/a
22	POLR2A	chr12:121647578-121648253	PFSK-1	brain:	n/a	n/a
23	CTCF	chr12:121647697-121647991	K562	blood:	n/a	chr12:121647877-121647890
24	GABPA	chr12:121647579-121648307	K562	blood:	n/a	chr12:121647953-121647962
25	TAF1	chr12:121647637-121648152	A549	lung:	n/a	n/a
26	RAD21	chr12:121647669-121648381	IMR90	lung:	n/a	n/a
27	JUND	chr12:121647711-121647957	H1-hESC	embryonic stem cell:	n/a	chr12:121647752-121647761
28	ELF1	chr12:121647590-121648373	GM12878	blood:	n/a	n/a
29	CTCF	chr12:121647840-121647990	NB4	blood:	n/a	chr12:121647877-121647890
30	ATF1	chr12:121647676-121648237	K562	blood:	n/a	chr12:121648086-121648100
31	POLR2A	chr12:121647607-121648402	HUVEC	blood vessel:	n/a	n/a
32	E2F6	chr12:121647583-121648584	A549	lung:	n/a	chr12:121647956-121647965
33	ELF1	chr12:121647666-121648289	K562	blood:	n/a	n/a
34	CTCF	chr12:121647740-121647890	Hela-S3	cervix:	n/a	chr12:121647877-121647890
35	POLR2A	chr12:121647696-121648406	HL-60	blood:	n/a	n/a
36	MTA3	chr12:121647771-121648204	GM12878	blood:	n/a	n/a
37	SP2	chr12:121647680-121647967	K562	blood:	n/a	chr12:121647856-121647871
38	RCOR1	chr12:121647811-121648459	Hela-S3	cervix:	n/a	n/a
39	YY1	chr12:121647576-121648266	GM12878	blood:	n/a	chr12:121647875-121647884 chr12:121647956-121647965 chr12:121647876-121647890 chr12:121647953-121647967
40	CTCF	chr12:121647820-121647970	MCF-7	breast:	n/a	chr12:121647877-121647890
41	USF1	chr12:121647744-121648040	SK-N-SH_RA	brain:	n/a	n/a
42	HA-E2F1	chr12:121647717-121648518	MCF-7	breast:	n/a	chr12:121647956-121647965
43	CTCF	chr12:121647760-121647910	HA-sp	spinal cord:	n/a	chr12:121647877-121647890
44	YY1	chr12:121647576-121648545	GM12892	blood:	n/a	chr12:121647875-121647884 chr12:121647956-121647965 chr12:121647876-121647890 chr12:121647953-121647967
45	POLR2A	chr12:121647422-121648716	HepG2	liver:	n/a	n/a
46	SIN3A	chr12:121647583-121648302	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr12:121647717-121648364	Raji	blood:	n/a	n/a
48	CTCF	chr12:121647740-121647890	Caco-2	colon:	n/a	chr12:121647877-121647890
49	CTCF	chr12:121647743-121648109	Pancreas_OC	pancreas:	n/a	chr12:121647877-121647890
50	MXI1	chr12:121647765-121648413	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121647374..121649635-chr12:121733730..121735639,2	K562	blood:
2	chr12:121647374..121649276-chr12:121733272..121735230,2	K562	blood:
3	chr12:121646473..121649457-chr12:121658577..121662737,5	MCF-7	breast:
4	chr12:121569906..121572539-chr12:121647803..121649868,2	MCF-7	breast:
5	chr12:121646670..121649250-chr12:121789949..121791934,2	K562	blood:
6	chr12:120965472..120968197-chr12:121646463..121648820,2	K562	blood:
7	chr12:121646675..121648577-chr16:89007038..89009106,2	MCF-7	breast:
8	chr12:121452592..121454438-chr12:121647839..121649379,2	MCF-7	breast:

Variant related genes	Relation type
P2RX4	TF binding region
ENSG00000110931	Chromatin interaction
ENSG00000089041	Chromatin interaction
ENSG00000135124	Chromatin interaction
ENSG00000089053	Chromatin interaction
ENSG00000129993	Chromatin interaction
ENSG00000157895	Chromatin interaction
ENSG00000110871	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11065484	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065496	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11541850	1.00[ASN][1000 genomes]
rs1169722	0.88[EUR][1000 genomes]
rs12321716	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17526121	1.00[ASN][1000 genomes]
rs1963773	1.00[ASN][1000 genomes]
rs56036638	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56067598	1.00[ASN][1000 genomes]
rs56110810	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56297690	1.00[ASN][1000 genomes]
rs6489796	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7136106	0.81[EUR][1000 genomes]
rs73220266	1.00[ASN][1000 genomes]
rs73220279	1.00[ASN][1000 genomes]
rs73220281	0.86[EUR][1000 genomes]
rs73220283	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73222413	0.83[AMR][1000 genomes]
rs9737637	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv899564	chr12:121641509-121689798	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv899565	chr12:121641509-121698785	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28360466	P2RX4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121643600-121648000	Weak transcription	Fetal Heart	heart
2	chr12:121647000-121648400	Enhancers	Fetal Brain Male	brain
3	chr12:121647000-121648400	Active TSS	Monocytes-CD14+_RO01746	blood
4	chr12:121647000-121648600	Active TSS	Primary T cells from cord blood	blood
5	chr12:121647000-121648600	Active TSS	Brain Substantia Nigra	brain
6	chr12:121647200-121648000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:121647200-121648400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:121647200-121648400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:121647200-121648400	Active TSS	Duodenum Mucosa	Duodenum
10	chr12:121647200-121648400	Active TSS	Fetal Brain Female	brain
11	chr12:121647200-121648400	Active TSS	Rectal Smooth Muscle	rectum
12	chr12:121647200-121648600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr12:121647200-121648600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:121647200-121648600	Active TSS	Brain Angular Gyrus	brain
15	chr12:121647200-121648600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:121647200-121648600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr12:121647200-121648600	Active TSS	A549	lung
18	chr12:121647200-121648600	Active TSS	Hela-S3	cervix
19	chr12:121647200-121648600	Active TSS	NHDF-Ad	bronchial
20	chr12:121647200-121649000	Active TSS	Small Intestine	intestine
21	chr12:121647200-121649400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr12:121647200-121649400	Active TSS	Colonic Mucosa	Colon
23	chr12:121647400-121648000	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr12:121647400-121648200	Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr12:121647400-121648200	Active TSS	Primary B cells from cord blood	blood
26	chr12:121647400-121648200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:121647400-121648400	Active TSS	H1 Cell Line	embryonic stem cell
28	chr12:121647400-121648400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:121647400-121648400	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr12:121647400-121648400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr12:121647400-121648400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:121647400-121648400	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr12:121647400-121648400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:121647400-121648400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:121647400-121648400	Active TSS	Brain Germinal Matrix	brain
36	chr12:121647400-121648400	Active TSS	Fetal Lung	lung
37	chr12:121647400-121648400	Active TSS	Fetal Stomach	stomach
38	chr12:121647400-121648400	Active TSS	HepG2	liver
39	chr12:121647400-121648400	Active TSS	Osteobl	bone
40	chr12:121647400-121648600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:121647400-121648600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:121647400-121648600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:121647400-121648600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:121647400-121648600	Active TSS	Brain Anterior Caudate	brain
45	chr12:121647400-121648600	Active TSS	Brain Hippocampus Middle	brain
46	chr12:121647400-121648600	Active TSS	Thymus	Thymus
47	chr12:121647400-121648600	Active TSS	GM12878-XiMat	blood
48	chr12:121647400-121648800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr12:121647400-121648800	Active TSS	Pancreas	Pancrea
50	chr12:121647400-121649000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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