Variant report

Variant	rs3024971
Chromosome Location	chr12:57493727-57493728
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	chr12:57493726-57493842	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr12:57493203-57494144	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:57493668-57494306	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:57493436-57494178	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr12:57493571-57494063	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:57493695-57493730	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:57493485-57494131	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:57493541-57493942	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:57493621-57494010	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:57493554-57493986	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:57493591-57494017	GM12891	blood:	n/a	n/a
12	POLR2A	chr12:57493545-57494036	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:57493202-57493981	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr12:57493708-57494087	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
STAT6	TF binding region

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1059513	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11172086	1.00[YRI][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
rs3024971	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	chr12:57487800-57494400	Strong transcription	Dnd41	blood
7	chr12:57487800-57495000	Strong transcription	Thymus	Thymus
8	chr12:57488200-57494800	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:57488400-57494000	Strong transcription	Left Ventricle	heart
10	chr12:57488400-57494200	Strong transcription	Fetal Lung	lung
11	chr12:57488400-57494400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:57488400-57495800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:57488600-57493800	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr12:57488600-57494000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:57488600-57494000	Strong transcription	Duodenum Mucosa	Duodenum
16	chr12:57488600-57494000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr12:57488600-57494200	Strong transcription	Rectal Smooth Muscle	rectum
18	chr12:57488600-57494400	Strong transcription	Colonic Mucosa	Colon
19	chr12:57488600-57494800	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:57488600-57494800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:57488600-57494800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:57488600-57495400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:57488600-57495800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:57488600-57495800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:57488600-57496600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:57488800-57493800	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr12:57488800-57494200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:57488800-57494400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:57488800-57494400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:57488800-57496000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr12:57488800-57496600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:57488800-57501400	Strong transcription	Adipose Nuclei	Adipose
33	chr12:57488800-57502400	Strong transcription	Fetal Stomach	stomach
34	chr12:57489000-57493800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:57489000-57494200	Strong transcription	Colon Smooth Muscle	Colon
36	chr12:57489000-57494800	Strong transcription	Liver	Liver
37	chr12:57489000-57495600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr12:57489000-57495800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr12:57489000-57496600	Strong transcription	NHLF	lung
40	chr12:57489000-57503600	Weak transcription	Brain Angular Gyrus	brain
41	chr12:57489200-57494800	Strong transcription	Primary B cells from cord blood	blood
42	chr12:57489200-57495800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr12:57489400-57494600	Strong transcription	Primary T cells from cord blood	blood
44	chr12:57489400-57494800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr12:57489400-57501400	Strong transcription	Lung	lung
46	chr12:57489400-57501600	Strong transcription	Ovary	ovary
47	chr12:57489600-57494400	Strong transcription	Primary hematopoietic stem cells	blood
48	chr12:57489600-57500200	Weak transcription	Fetal Kidney	kidney
49	chr12:57489800-57494400	Genic enhancers	Fetal Muscle Leg	muscle
50	chr12:57489800-57496200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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