Variant report

Variant	rs870392
Chromosome Location	chr12:58219173-58219174
allele	A/C
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	POLR2A	chr12:58218775-58219234	K562	blood:	n/a	n/a
2	ZNF263	chr12:58219001-58219555	HEK293-T-REx	kidney:	n/a	chr12:58219192-58219213
3	POLR2A	chr12:58212030-58219642	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:58209632-58221838	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58219013..58221062-chr12:58238426..58242369,4	K562	blood:
2	chr12:58211567..58213701-chr12:58218722..58220729,2	MCF-7	breast:
3	chr12:58217743..58220104-chr12:58222008..58224494,2	MCF-7	breast:
4	chr12:58218535..58220523-chr12:58222880..58224447,2	K562	blood:

Variant related genes	Relation type
CTDSP2	TF binding region
MIR26A2	TF binding region
ENSG00000175215	Chromatin interaction
ENSG00000135407	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1021469	0.83[JPT][hapmap]
rs10431552	0.88[JPT][hapmap]
rs10444569	0.82[AMR][1000 genomes]
rs10747783	0.88[JPT][hapmap]
rs10747784	0.81[EUR][1000 genomes]
rs10747786	0.83[CHD][hapmap];0.94[JPT][hapmap]
rs10747787	0.83[CHD][hapmap];0.94[JPT][hapmap]
rs10783847	0.88[JPT][hapmap]
rs10783848	0.86[JPT][hapmap]
rs10783850	0.87[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783851	0.87[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10783853	0.86[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10783854	0.87[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10783855	0.88[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10783856	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10877011	1.00[YRI][hapmap]
rs10877012	0.88[JPT][hapmap]
rs10877013	0.81[JPT][hapmap]
rs10877014	0.88[JPT][hapmap]
rs10877015	0.88[JPT][hapmap]
rs10877016	0.88[JPT][hapmap]
rs10877019	0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap]
rs10877022	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877024	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877025	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877026	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10877028	0.88[CEU][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap]
rs10877029	0.83[CHD][hapmap];0.94[JPT][hapmap]
rs10877030	0.83[CHD][hapmap];0.94[JPT][hapmap]
rs10877031	0.82[AMR][1000 genomes]
rs11172333	0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11172335	0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11172343	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs11172344	0.88[JPT][hapmap]
rs11172349	0.84[CHB][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11172351	0.84[CHB][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap]
rs11172361	0.81[EUR][1000 genomes]
rs11172362	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172367	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs11172369	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11172371	1.00[YRI][hapmap]
rs12426201	0.82[AMR][1000 genomes]
rs1599750	0.88[CEU][hapmap];0.90[CHD][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1599751	0.88[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1599931	0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs1875124	0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1875125	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2002275	0.86[ASW][hapmap];0.87[MEX][hapmap]
rs2069502	0.83[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap]
rs2072052	0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs3825079	0.84[CHB][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4237844	0.87[ASW][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes]
rs4646536	0.88[JPT][hapmap]
rs4760171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760172	0.87[CHD][hapmap];0.94[JPT][hapmap]
rs4760332	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760333	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760335	0.82[EUR][1000 genomes]
rs4760339	0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs4760340	0.81[CHD][hapmap]
rs4760341	0.94[JPT][hapmap];0.85[YRI][hapmap]
rs5017863	0.83[AMR][1000 genomes]
rs6581155	0.88[JPT][hapmap]
rs703842	0.88[JPT][hapmap]
rs724834	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs7312623	0.83[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs7489290	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8181644	0.88[JPT][hapmap]
rs871871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923829	0.88[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs870392	GPR84	cis	cerebellum	SCAN
rs870392	DKFZP586D0919	cis	multi-tissue	Pritchard
rs870392	TSPAN31	cis	parietal	SCAN
rs870392	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs870392	FAM119B	cis	Cerebellum	GTEx
rs870392	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs870392	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs870392	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs870392	METTL21B	cis	Esophagus Muscularis	GTEx
rs870392	FAM119B	cis	cerebellum	SCAN
rs870392	FAM119B	cis	lymphoblastoid	seeQTL
rs870392	FAM119B	cis	Lymphoblastoid	GTEx
rs870392	TSFM	cis	cerebellum	SCAN
rs870392	TSFM	cis	multi-tissue	Pritchard
rs870392	MUCL1	cis	parietal	SCAN
rs870392	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs870392	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs870392	METTL21B	cis	Whole Blood	GTEx
rs870392	PPP1R1A	cis	parietal	SCAN
rs870392	FAM119B	cis	parietal	SCAN
rs870392	KRT8	cis	cerebellum	SCAN
rs870392	XRCC6BP1	cis	Whole Blood	GTEx
rs870392	METTL21B	cis	Muscle Skeletal	GTEx
rs870392	XRCC6BP1	cis	Artery Tibial	GTEx
rs870392	TSPAN31	cis	cerebellum	SCAN
rs870392	CDK2	cis	parietal	SCAN
rs870392	TSFM	cis	lymphoblastoid	seeQTL
rs870392	XRCC6BP1	cis	lung	GTEx
rs870392	FAM119B	cis	Temporal Cortex	GTEx
rs870392	FAM119B	cis	Frontal Cortex	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58207800-58222800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:58209400-58226800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:58211200-58223800	Strong transcription	Osteobl	bone
4	chr12:58211400-58224600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:58211400-58224800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:58211600-58222800	Strong transcription	Fetal Stomach	stomach
7	chr12:58211600-58224000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:58212000-58222600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:58212000-58222800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:58212000-58224400	Strong transcription	Fetal Intestine Large	intestine
11	chr12:58212000-58224800	Strong transcription	Thymus	Thymus
12	chr12:58212200-58222800	Strong transcription	Fetal Intestine Small	intestine
13	chr12:58212200-58223600	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:58212200-58223800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:58212200-58224800	Strong transcription	Brain Germinal Matrix	brain
16	chr12:58212400-58222600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:58212400-58222600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:58212400-58222800	Strong transcription	Primary hematopoietic stem cells	blood
19	chr12:58212400-58222800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:58212400-58223600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:58212400-58223600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:58212600-58222800	Strong transcription	Brain Cingulate Gyrus	brain
23	chr12:58212600-58223200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr12:58212600-58224000	Strong transcription	Fetal Lung	lung
25	chr12:58212600-58224200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:58213000-58222000	Strong transcription	Brain Substantia Nigra	brain
27	chr12:58213000-58223200	Strong transcription	NHLF	lung
28	chr12:58213000-58223400	Strong transcription	Fetal Brain Female	brain
29	chr12:58213200-58222800	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:58213400-58220800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr12:58213400-58223000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:58213400-58223000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:58213400-58223000	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:58213400-58223200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr12:58213400-58224000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr12:58213600-58223000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:58213600-58224000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:58213600-58224400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:58213800-58220800	Strong transcription	Colon Smooth Muscle	Colon
40	chr12:58213800-58222400	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr12:58213800-58224000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:58214000-58220000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr12:58214000-58222600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:58214000-58222800	Strong transcription	Brain Hippocampus Middle	brain
45	chr12:58214000-58223000	Strong transcription	Brain Angular Gyrus	brain
46	chr12:58214000-58223800	Strong transcription	Primary B cells from cord blood	blood
47	chr12:58214200-58223000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr12:58214400-58223000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:58214400-58223200	Strong transcription	Primary T cells from cord blood	blood
50	chr12:58214400-58223200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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