Variant report

Variant	rs3176787
Chromosome Location	chr12:9913134-9913135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9911841..9913386-chr15:75626796..75629436,2	K562	blood:
2	chr12:9911685..9913849-chr12:10017850..10019855,2	K562	blood:

Variant related genes	Relation type
ENSG00000255882	Chromatin interaction
ENSG00000140365	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1029990	0.94[ASN][1000 genomes]
rs1029991	0.94[ASN][1000 genomes]
rs1029992	0.94[ASN][1000 genomes]
rs1029993	0.94[ASN][1000 genomes]
rs1029994	0.94[ASN][1000 genomes]
rs10772127	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772128	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772132	0.94[ASN][1000 genomes]
rs10772138	0.86[JPT][hapmap]
rs10844737	0.95[ASN][1000 genomes]
rs10844749	0.94[ASN][1000 genomes]
rs10844750	0.94[ASN][1000 genomes]
rs10844769	0.86[JPT][hapmap]
rs11052969	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11052970	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11052971	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11052978	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12422685	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12422688	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12422955	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12422989	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12425365	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12427030	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12427278	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12427301	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12582052	0.94[ASN][1000 genomes]
rs12816871	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12817268	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12819552	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12824297	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12824308	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1540355	0.94[ASN][1000 genomes]
rs1540356	0.94[ASN][1000 genomes]
rs1861090	0.94[ASN][1000 genomes]
rs2071647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2110449	0.86[JPT][hapmap]
rs2110450	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2110451	0.94[ASN][1000 genomes]
rs2160086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3136559	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3136563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3176773	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3176775	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3176776	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3176789	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs34779650	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35143542	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35559880	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4385980	0.94[ASN][1000 genomes]
rs4519175	0.94[ASN][1000 genomes]
rs4519176	0.94[ASN][1000 genomes]
rs724666	0.95[ASN][1000 genomes]
rs724667	0.94[ASN][1000 genomes]
rs724668	0.95[ASN][1000 genomes]
rs7295897	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7309767	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7309875	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7488011	0.94[ASN][1000 genomes]
rs7953260	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7958251	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9971740	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][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	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3176787	GPR19	cis	cerebellum	SCAN
rs3176787	LEPREL2	cis	parietal	SCAN
rs3176787	TAS2R19	cis	cerebellum	SCAN
rs3176787	CLEC6A	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9903400-9917600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:9904400-9913200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:9904600-9913400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
4	chr12:9905600-9913400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:9909000-9914800	Active TSS	Thymus	Thymus
6	chr12:9909600-9913400	Active TSS	Fetal Thymus	thymus
7	chr12:9909600-9914200	Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr12:9909800-9914000	Active TSS	K562	blood
9	chr12:9909800-9914400	Active TSS	Primary T cells fromperipheralblood	blood
10	chr12:9910200-9914200	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr12:9910400-9913600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:9910400-9914000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr12:9910400-9914400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:9910400-9914400	Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr12:9910600-9913600	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr12:9910600-9913600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr12:9910600-9914400	Active TSS	Primary T cells from cord blood	blood
18	chr12:9910600-9914400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:9910800-9913400	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr12:9911000-9913800	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr12:9911000-9914000	Active TSS	Duodenum Mucosa	Duodenum
22	chr12:9911200-9913600	Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr12:9911200-9913600	Active TSS	Rectal Smooth Muscle	rectum
24	chr12:9911200-9913600	Active TSS	GM12878-XiMat	blood
25	chr12:9911400-9913400	Active TSS	Primary B cells from cord blood	blood
26	chr12:9911400-9913600	Active TSS	Primary B cells from peripheral blood	blood
27	chr12:9911400-9913600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:9911400-9913600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:9911600-9913400	Active TSS	Primary hematopoietic stem cells	blood
30	chr12:9911600-9913400	Weak transcription	Placenta	Placenta
31	chr12:9912000-9914200	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr12:9912200-9913200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
33	chr12:9912200-9913200	Active TSS	Fetal Stomach	stomach
34	chr12:9912600-9913200	Active TSS	Monocytes-CD14+_RO01746	blood
35	chr12:9912600-9913400	Active TSS	HUVEC	blood vessel
36	chr12:9912600-9914000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:9912800-9913600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:9912800-9913800	Active TSS	Adipose Nuclei	Adipose
39	chr12:9912800-9914200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:9912800-9915000	Flanking Active TSS	Dnd41	blood
41	chr12:9913000-9916000	Enhancers	Primary monocytes fromperipheralblood	blood

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