Variant report

Variant	rs3024974
Chromosome Location	chr12:57492745-57492746
allele	C/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	POLR2A	chr12:57492212-57493109	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:57492636-57493413	U87	brain:	n/a	n/a
3	POLR2A	chr12:57492304-57492842	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr12:57492687-57493302	U87	brain:	n/a	n/a
5	POLR2A	chr12:57491920-57493468	GM12891	blood:	n/a	n/a
6	POLR2A	chr12:57492415-57493054	HL-60	blood:	n/a	n/a
7	POLR2A	chr12:57492427-57493102	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:57491994-57493019	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:57492557-57493085	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:57492656-57493160	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:57492669-57492958	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:57492370-57493097	GM12892	blood:	n/a	n/a
13	POLR2A	chr12:57492425-57492968	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
STAT6	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1044939	0.90[CEU][hapmap];0.80[CHB][hapmap]
rs10506350	0.92[CHD][hapmap]
rs10506351	0.90[CEU][hapmap];0.80[CHB][hapmap]
rs12099695	0.81[CEU][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap]
rs12810024	0.84[CHD][hapmap]
rs1552245	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17119301	0.92[CHD][hapmap]
rs17119327	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17119330	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17119344	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17119386	0.90[CEU][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17119388	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17119390	0.88[CEU][hapmap];0.80[CHB][hapmap]
rs17119407	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17119416	0.90[CEU][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17119418	0.90[CEU][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs17119494	0.88[JPT][hapmap]
rs2035545	1.00[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2233267	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2270736	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap]
rs2270737	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap]
rs2270739	0.80[CHB][hapmap]
rs2279373	0.81[CEU][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap]
rs2279743	0.92[CHD][hapmap]
rs2291855	0.80[CHB][hapmap]
rs2371717	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs3024975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35493121	0.81[CEU][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap]
rs3759134	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3759135	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3782329	0.85[CEU][hapmap];0.80[CHB][hapmap]
rs3782330	0.90[CEU][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap]
rs3803018	0.90[CEU][hapmap];0.92[CHD][hapmap];0.90[MEX][hapmap]
rs4016338	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs4039	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs4143085	0.90[CEU][hapmap]
rs66741626	0.81[ASN][1000 genomes]
rs7136770	0.92[CHD][hapmap]
rs7298475	0.90[CEU][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs73118413	0.83[AMR][1000 genomes]
rs73118416	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73118418	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73118432	0.99[EUR][1000 genomes]
rs733629	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs746049	0.92[CHD][hapmap]
rs7961920	0.80[CHB][hapmap];0.92[CHD][hapmap]
rs7962771	0.90[CEU][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs7972615	0.90[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs901068	0.92[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers 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	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3024974	STAT6	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57484000-57498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:57486200-57503600	Weak transcription	Fetal Brain Male	brain
3	chr12:57486600-57503800	Weak transcription	Brain Substantia Nigra	brain
4	chr12:57487600-57501400	Weak transcription	Right Atrium	heart
5	chr12:57487600-57503600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:57487800-57493000	Strong transcription	Brain Hippocampus Middle	brain
7	chr12:57487800-57494400	Strong transcription	Dnd41	blood
8	chr12:57487800-57495000	Strong transcription	Thymus	Thymus
9	chr12:57488200-57494800	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:57488400-57493000	Genic enhancers	K562	blood
11	chr12:57488400-57494000	Strong transcription	Left Ventricle	heart
12	chr12:57488400-57494200	Strong transcription	Fetal Lung	lung
13	chr12:57488400-57494400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:57488400-57495800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:57488600-57493800	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr12:57488600-57494000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:57488600-57494000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr12:57488600-57494000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr12:57488600-57494200	Strong transcription	Rectal Smooth Muscle	rectum
20	chr12:57488600-57494400	Strong transcription	Colonic Mucosa	Colon
21	chr12:57488600-57494800	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:57488600-57494800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:57488600-57494800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:57488600-57495400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr12:57488600-57495800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:57488600-57495800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:57488600-57496600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:57488800-57493000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:57488800-57493000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:57488800-57493800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr12:57488800-57494200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:57488800-57494400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:57488800-57494400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:57488800-57496000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr12:57488800-57496600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:57488800-57501400	Strong transcription	Adipose Nuclei	Adipose
37	chr12:57488800-57502400	Strong transcription	Fetal Stomach	stomach
38	chr12:57489000-57493800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:57489000-57494200	Strong transcription	Colon Smooth Muscle	Colon
40	chr12:57489000-57494800	Strong transcription	Liver	Liver
41	chr12:57489000-57495600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr12:57489000-57495800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr12:57489000-57496600	Strong transcription	NHLF	lung
44	chr12:57489000-57503600	Weak transcription	Brain Angular Gyrus	brain
45	chr12:57489200-57494800	Strong transcription	Primary B cells from cord blood	blood
46	chr12:57489200-57495800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr12:57489400-57493400	Genic enhancers	NHDF-Ad	bronchial
48	chr12:57489400-57494600	Strong transcription	Primary T cells from cord blood	blood
49	chr12:57489400-57494800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
50	chr12:57489400-57501400	Strong transcription	Lung	lung

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