Variant report

Variant	rs1653622
Chromosome Location	chr12:121647435-121647436
allele	A/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	CCNT2	chr12:121647421-121648519	K562	blood:	n/a	n/a
2	POLR2A	chr12:121647422-121648716	HepG2	liver:	n/a	n/a
3	CBX3	chr12:121647381-121648621	K562	blood:	n/a	n/a
4	CTCF	chr12:121647366-121649096	A549	lung:	n/a	chr12:121647877-121647890
5	MXI1	chr12:121647198-121648795	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr12:121647340-121648349	HCT-116	colon:	n/a	n/a
7	POLR2A	chr12:121647014-121648829	K562	blood:	n/a	n/a
8	ELF1	chr12:121647372-121648483	GM12878	blood:	n/a	n/a
9	MXI1	chr12:121647423-121648921	IMR90	lung:	n/a	n/a
10	REST	chr12:121647404-121648781	H1-neurons	neurons:	n/a	n/a
11	MAZ	chr12:121647218-121648591	IMR90	lung:	n/a	chr12:121648179-121648190
12	ZNF384	chr12:121647328-121647957	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:121647390-121648699	K562	blood:	n/a	n/a
14	RAD21	chr12:121647423-121648336	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr12:121647375-121648100	HCT-116	colon:	n/a	chr12:121647877-121647890
16	E2F6	chr12:121647409-121647526	K562	blood:	n/a	n/a
17	ZNF384	chr12:121646928-121648317	K562	blood:	n/a	n/a
18	CTCF	chr12:121647377-121648209	HCT-116	colon:	n/a	chr12:121647877-121647890
19	MAX	chr12:121647369-121648684	K562	blood:	n/a	chr12:121648179-121648190
20	MAX	chr12:121647366-121648703	A549	lung:	n/a	chr12:121648179-121648190
21	HCFC1	chr12:121647423-121648729	Hela-S3	cervix:	n/a	n/a
22	JUN	chr12:121647187-121649065	K562	blood:	n/a	chr12:121647752-121647761
23	RAD21	chr12:121647294-121648459	SK-N-SH	brain:	n/a	n/a
24	HCFC1	chr12:121647332-121648692	K562	blood:	n/a	n/a
25	POLR2A	chr12:121647416-121648423	MCF10A-Er-Src	breast:	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	chr12:121646670..121649250-chr12:121789949..121791934,2	K562	blood:
5	chr12:120965472..120968197-chr12:121646463..121648820,2	K562	blood:
6	chr12:121646675..121648577-chr16:89007038..89009106,2	MCF-7	breast:
7	chr12:121547509..121549908-chr12:121645627..121647537,2	MCF-7	breast:

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

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10774587	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10774589	0.95[JPT][hapmap]
rs10849852	0.84[AFR][1000 genomes]
rs10849855	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10849856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10849858	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11065479	0.92[AMR][1000 genomes]
rs11065486	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1180051	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1182945	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1629287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1653623	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1718117	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071271	0.84[ASN][1000 genomes]
rs2393849	0.87[ASN][1000 genomes]
rs2393850	0.85[ASN][1000 genomes]
rs25643	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs2567978	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2567980	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2567993	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2567994	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668235	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2668252	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2686362	0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2686363	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2686387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686388	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2942063	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58232824	0.87[ASN][1000 genomes]
rs6489799	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs725135	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7298368	0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs930186	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs930187	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1653622	P2RX4	cis	lymphoblastoid	seeQTL
rs1653622	PSMD9	cis	parietal	SCAN
rs1653622	P2RX4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121641400-121647800	Weak transcription	Gastric	stomach
2	chr12:121643000-121647600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:121643600-121648000	Weak transcription	Fetal Heart	heart
4	chr12:121646800-121647600	Enhancers	Primary hematopoietic stem cells	blood
5	chr12:121646800-121647600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:121647000-121647600	Enhancers	Lung	lung
7	chr12:121647000-121647600	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr12:121647000-121647600	Flanking Active TSS	Dnd41	blood
9	chr12:121647000-121647600	Flanking Active TSS	K562	blood
10	chr12:121647000-121647800	Flanking Active TSS	Placenta	Placenta
11	chr12:121647000-121648400	Enhancers	Fetal Brain Male	brain
12	chr12:121647000-121648400	Active TSS	Monocytes-CD14+_RO01746	blood
13	chr12:121647000-121648600	Active TSS	Primary T cells from cord blood	blood
14	chr12:121647000-121648600	Active TSS	Brain Substantia Nigra	brain
15	chr12:121647200-121647600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:121647200-121647600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:121647200-121647600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr12:121647200-121647600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:121647200-121647600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:121647200-121647600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:121647200-121647600	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr12:121647200-121647600	Enhancers	Liver	Liver
23	chr12:121647200-121647600	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr12:121647200-121647600	Flanking Active TSS	Fetal Intestine Large	intestine
25	chr12:121647200-121647600	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr12:121647200-121647600	Enhancers	Psoas Muscle	Psoas
27	chr12:121647200-121647600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr12:121647200-121647600	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr12:121647200-121647600	Enhancers	HUVEC	blood vessel
30	chr12:121647200-121647800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr12:121647200-121647800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr12:121647200-121647800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:121647200-121647800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr12:121647200-121647800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr12:121647200-121648000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:121647200-121648400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:121647200-121648400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:121647200-121648400	Active TSS	Duodenum Mucosa	Duodenum
39	chr12:121647200-121648400	Active TSS	Fetal Brain Female	brain
40	chr12:121647200-121648400	Active TSS	Rectal Smooth Muscle	rectum
41	chr12:121647200-121648600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
42	chr12:121647200-121648600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:121647200-121648600	Active TSS	Brain Angular Gyrus	brain
44	chr12:121647200-121648600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:121647200-121648600	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr12:121647200-121648600	Active TSS	A549	lung
47	chr12:121647200-121648600	Active TSS	Hela-S3	cervix
48	chr12:121647200-121648600	Active TSS	NHDF-Ad	bronchial
49	chr12:121647200-121649000	Active TSS	Small Intestine	intestine
50	chr12:121647200-121649400	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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