Variant report

Variant	rs2001881
Chromosome Location	chr4:53993103-53993104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53987651..53991411-chr4:53993052..53996048,3	K562	blood:
2	chr4:53979124..53981859-chr4:53991405..53994171,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11133246	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11133247	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11929903	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap]
rs11939189	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes]
rs12108246	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs12499016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12507228	0.84[AMR][1000 genomes]
rs12512359	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12640471	0.84[AMR][1000 genomes]
rs12650397	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17082453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17082476	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17082504	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs17082529	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs17082565	0.85[CHB][hapmap]
rs1987028	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4421047	0.82[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap]
rs4515221	0.84[AMR][1000 genomes]
rs4864451	0.85[CHB][hapmap]
rs4864453	0.85[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs4864747	0.85[CHB][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap]
rs6826467	0.85[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs6833592	0.83[ASN][1000 genomes]
rs72624192	0.87[AMR][1000 genomes]
rs72624193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72624194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73143456	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73143458	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73143484	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs751265	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs7688646	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs7696426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2001881	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53978800-54008000	Weak transcription	Primary T cells from cord blood	blood
2	chr4:53986200-53993200	Weak transcription	Fetal Kidney	kidney
3	chr4:53986200-53993600	Weak transcription	Psoas Muscle	Psoas
4	chr4:53986600-53993600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:53986600-53994600	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:53986800-54010800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:53986800-54011000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:53987600-53993600	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:53987800-53993600	Weak transcription	Aorta	Aorta
10	chr4:53987800-53993800	Weak transcription	Adipose Nuclei	Adipose
11	chr4:53987800-54016800	Weak transcription	NHLF	lung
12	chr4:53988000-53993800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:53988000-53994400	Weak transcription	NHDF-Ad	bronchial
14	chr4:53988000-53997600	Weak transcription	Osteobl	bone
15	chr4:53988200-54008000	Weak transcription	Primary B cells from cord blood	blood
16	chr4:53988600-54011000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:53988800-53993600	Weak transcription	Right Atrium	heart
18	chr4:53989200-54010200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr4:53989600-53995000	Weak transcription	Brain Substantia Nigra	brain
20	chr4:53990000-53993400	Weak transcription	Fetal Intestine Large	intestine
21	chr4:53990000-53995000	Weak transcription	HUVEC	blood vessel
22	chr4:53990400-53995000	Weak transcription	Liver	Liver
23	chr4:53992400-54009600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:53992800-53993600	Weak transcription	Left Ventricle	heart
25	chr4:53992800-53994600	Enhancers	Fetal Lung	lung
26	chr4:53992800-53995400	Enhancers	Ovary	ovary
27	chr4:53993000-53993800	Enhancers	Fetal Stomach	stomach

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