Variant report

Variant	rs6535590
Chromosome Location	chr4:149127801-149127802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11099680	0.80[ASN][1000 genomes]
rs11099681	0.84[CEU][hapmap];0.87[CHB][hapmap];0.80[ASN][1000 genomes]
rs11099682	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13103165	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2356393	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3843410	0.80[CHB][hapmap]
rs3843411	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs3843413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3846304	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846305	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3857079	0.82[CHB][hapmap]
rs3910052	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]
rs3910053	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3910054	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3910056	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3910057	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4122852	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4835491	0.82[CHB][hapmap]
rs4835493	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs4835495	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4835496	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4835500	0.95[ASN][1000 genomes]
rs4835501	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4835504	0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4835505	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4835506	0.93[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535589	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6535591	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6535593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535594	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6820751	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6828665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6841570	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6846591	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7656855	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7670108	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7673644	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv1027263	chr4:149127120-149320135	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv537296	chr4:149127120-149320135	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers	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
rs6535590	MMAA	cis	cerebellum	SCAN

Chromatin state (count:24 , 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	chr4:149125600-149132000	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:149126000-149135600	Weak transcription	Brain Substantia Nigra	brain
18	chr4:149126000-149136600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:149126200-149135400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:149126400-149131200	Weak transcription	Fetal Kidney	kidney
21	chr4:149127000-149135400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:149127200-149132000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:149127200-149132200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:149127600-149128400	Enhancers	Fetal Heart	heart

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