Variant report

Variant	rs838637
Chromosome Location	chr3:143199051-143199052
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1525007	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525009	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723033	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2140765	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66623546	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708484	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73144723	1.00[ASN][1000 genomes]
rs838599	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838602	0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs838613	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838616	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838618	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838620	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838623	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838627	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838630	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838634	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838635	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838643	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838644	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838646	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838648	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838649	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs865710	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289661	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs838637	CRCT1	trans	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143159600-143200800	Weak transcription	Esophagus	oesophagus
2	chr3:143163800-143203400	Weak transcription	Ovary	ovary
3	chr3:143174400-143220400	Weak transcription	Fetal Lung	lung
4	chr3:143176800-143220400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:143177200-143200800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:143177800-143204400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:143178000-143203200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:143179400-143220400	Weak transcription	Brain Substantia Nigra	brain
9	chr3:143179800-143213400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:143180200-143200600	Weak transcription	Aorta	Aorta
11	chr3:143185800-143213800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:143186000-143201200	Weak transcription	Adipose Nuclei	Adipose
13	chr3:143186000-143215600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:143186000-143223000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:143186400-143204400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:143191200-143211000	Weak transcription	Primary T cells from cord blood	blood
17	chr3:143191400-143231000	Weak transcription	Primary B cells from cord blood	blood
18	chr3:143192400-143211400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr3:143192400-143215200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr3:143196600-143200200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr3:143196600-143203800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:143197000-143202800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:143197400-143199400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:143197400-143201200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:143197400-143201600	Weak transcription	Fetal Stomach	stomach
26	chr3:143197400-143203800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:143197800-143202200	Enhancers	HSMM	muscle
28	chr3:143198400-143199600	Enhancers	Dnd41	blood
29	chr3:143198600-143199600	Enhancers	Fetal Kidney	kidney
30	chr3:143198600-143199600	Enhancers	HSMMtube	muscle
31	chr3:143198600-143199600	Enhancers	HUVEC	blood vessel
32	chr3:143198600-143199800	Enhancers	Colonic Mucosa	Colon
33	chr3:143198600-143199800	Enhancers	Fetal Intestine Small	intestine
34	chr3:143198600-143199800	Enhancers	A549	lung
35	chr3:143198600-143199800	Enhancers	Osteobl	bone
36	chr3:143198600-143201600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:143198600-143202200	Enhancers	NHDF-Ad	bronchial
38	chr3:143198800-143199400	Enhancers	Primary B cells from peripheral blood	blood
39	chr3:143198800-143199600	Enhancers	Fetal Thymus	thymus
40	chr3:143198800-143199600	Enhancers	NH-A	brain
41	chr3:143198800-143199800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:143198800-143199800	Enhancers	Duodenum Mucosa	Duodenum
43	chr3:143198800-143199800	Enhancers	Fetal Intestine Large	intestine
44	chr3:143198800-143199800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr3:143198800-143199800	Enhancers	Stomach Mucosa	stomach
46	chr3:143199000-143199200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr3:143199000-143199200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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