Variant report

Variant	rs2950852
Chromosome Location	chr5:90409081-90409082
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90408615..90411255-chr5:90413057..90415567,2	K562	blood:
2	chr5:90407899..90410554-chr5:90411304..90413710,2	K562	blood:
3	chr5:90405497..90409184-chr5:90675252..90678679,4	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12109264	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16869403	0.81[AMR][1000 genomes]
rs16869404	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs16869414	0.81[CEU][hapmap];1.00[MEX][hapmap]
rs16869425	0.91[CEU][hapmap];0.84[CHD][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1852731	0.91[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1876635	0.88[MEX][hapmap]
rs1986718	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950849	0.91[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2950850	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950851	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950854	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2950855	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973444	0.81[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973445	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973447	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973448	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973449	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973453	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973454	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973455	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973456	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112484	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3952745	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56377639	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58524182	0.87[AMR][1000 genomes]
rs59654682	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59661306	0.80[AMR][1000 genomes]
rs66482530	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs66608099	0.81[AMR][1000 genomes]
rs6874106	0.81[CEU][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs73189007	1.00[ASN][1000 genomes]
rs73189008	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2950852	MCTP1	cis	cerebellum	SCAN
rs2950852	RASA1	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90395400-90415200	Weak transcription	Left Ventricle	heart
2	chr5:90396200-90422800	Weak transcription	Esophagus	oesophagus
3	chr5:90401600-90431800	Weak transcription	K562	blood
4	chr5:90402400-90413600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:90403000-90415600	Weak transcription	Right Atrium	heart
6	chr5:90403000-90431600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:90403200-90431600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:90403400-90418800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:90403400-90418800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:90405800-90410800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:90406200-90409200	Enhancers	Fetal Brain Female	brain
12	chr5:90406600-90409400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr5:90406600-90421800	Weak transcription	Small Intestine	intestine
14	chr5:90406800-90414000	Weak transcription	Fetal Lung	lung
15	chr5:90406800-90418600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:90407200-90410400	Weak transcription	Fetal Stomach	stomach
17	chr5:90407200-90415800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:90407600-90410400	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:90407600-90415000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:90407600-90416000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:90407800-90410400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:90407800-90410600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:90407800-90414400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:90408000-90410000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr5:90408000-90410000	Weak transcription	Fetal Muscle Leg	muscle
26	chr5:90408000-90410400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:90408000-90410400	Weak transcription	Adipose Nuclei	Adipose
28	chr5:90408000-90410400	Weak transcription	Fetal Heart	heart
29	chr5:90408000-90410400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr5:90408200-90410200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr5:90408200-90410400	Weak transcription	Brain Anterior Caudate	brain
32	chr5:90408200-90410400	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:90408200-90410400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr5:90408200-90413600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:90408200-90414600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:90408400-90410400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:90408800-90409200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr5:90409000-90409200	Enhancers	Brain Germinal Matrix	brain

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