Variant report

Variant	rs3910052
Chromosome Location	chr4:149126915-149126916
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	chr4:149126460-149126945	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
NR3C2	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11099681	0.84[CEU][hapmap];0.80[CHB][hapmap];0.82[GIH][hapmap]
rs11099682	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13103165	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2356393	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3843411	0.81[CEU][hapmap];0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs3843413	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3846304	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3910053	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3910054	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3910056	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3910057	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4122852	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4835493	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs4835495	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4835496	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4835500	0.99[ASN][1000 genomes]
rs4835501	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4835503	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835504	0.90[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835505	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835506	0.93[CHB][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6535589	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6535590	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6535591	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6535593	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6535594	0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[ASN][1000 genomes]
rs6820751	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6828665	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6841570	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6846591	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7656855	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670108	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7673644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[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	nsv1032794	chr4:149046598-149135489	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv537295	chr4:149046598-149135489	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3910052	MMAA	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:149112400-149137400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr4:149114200-149131400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:149115800-149137400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:149117200-149138000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr4:149123600-149150200	Weak transcription	Right Ventricle	heart
6	chr4:149124000-149131600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:149124000-149133200	Weak transcription	Left Ventricle	heart
8	chr4:149124000-149133400	Weak transcription	Pancreas	Pancrea
9	chr4:149124000-149136400	Weak transcription	Brain Angular Gyrus	brain
10	chr4:149125000-149132800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:149125000-149133400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:149125000-149135600	Weak transcription	Ovary	ovary
13	chr4:149125200-149130400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:149125200-149132800	Weak transcription	Aorta	Aorta
15	chr4:149125200-149136000	Weak transcription	Psoas Muscle	Psoas
16	chr4:149125600-149127000	Weak transcription	Brain Anterior Caudate	brain
17	chr4:149125600-149127000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr4:149125600-149127200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:149125600-149132000	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:149126000-149135600	Weak transcription	Brain Substantia Nigra	brain
21	chr4:149126000-149136600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:149126200-149135400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:149126400-149127200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:149126400-149127200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr4:149126400-149131200	Weak transcription	Fetal Kidney	kidney
26	chr4:149126600-149127000	Enhancers	Liver	Liver
27	chr4:149126600-149127000	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr4:149126600-149127400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:149126800-149127400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr4:149126800-149127600	Weak transcription	Fetal Heart	heart

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