Variant report

Variant	rs7696426
Chromosome Location	chr4:54008839-54008840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53998244..54000352-chr4:54008582..54010279,2	K562	blood:
2	chr4:54007557..54010483-chr4:54011201..54014968,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11133246	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11133247	0.91[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];0.88[MEX][hapmap]
rs11939189	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap]
rs12108246	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs12499016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12507228	0.81[AMR][1000 genomes]
rs12512359	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12640471	0.81[AMR][1000 genomes]
rs12650397	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13141154	0.80[YRI][hapmap]
rs17082453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17082476	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[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];0.89[MEX][hapmap]
rs17082529	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs17082565	0.85[CHB][hapmap]
rs1987028	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2001881	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]
rs2368380	0.84[YRI][hapmap]
rs4421047	0.82[CEU][hapmap];0.93[CHB][hapmap]
rs4515221	0.81[AMR][1000 genomes]
rs4864447	1.00[YRI][hapmap]
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];0.93[GIH][hapmap];0.94[MEX][hapmap]
rs6554066	1.00[YRI][hapmap]
rs6826467	0.85[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs6833592	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72624192	0.84[AMR][1000 genomes]
rs72624193	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72624194	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73143456	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73143458	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73143484	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs751265	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];0.89[MEX][hapmap]

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
rs7696426	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53986800-54010800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:53986800-54011000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:53987800-54016800	Weak transcription	NHLF	lung
4	chr4:53988600-54011000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:53989200-54010200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr4:53992400-54009600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:53993800-54027800	Weak transcription	Fetal Stomach	stomach
8	chr4:53994000-54011000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:53995200-54014800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:53995400-54017800	Weak transcription	Brain Substantia Nigra	brain
11	chr4:53997000-54017600	Weak transcription	Gastric	stomach
12	chr4:53997400-54020000	Weak transcription	HSMM	muscle
13	chr4:53997800-54011000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:53998000-54010800	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:53998000-54011000	Weak transcription	Left Ventricle	heart
16	chr4:53998400-54010200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:53998600-54014400	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:53998800-54010400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:53999000-54010200	Weak transcription	Osteobl	bone
20	chr4:53999000-54011000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:53999000-54013200	Weak transcription	Brain Angular Gyrus	brain
22	chr4:53999000-54017200	Weak transcription	Fetal Lung	lung
23	chr4:53999000-54027800	Weak transcription	NHDF-Ad	bronchial
24	chr4:53999200-54009600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr4:53999200-54011000	Weak transcription	Adipose Nuclei	Adipose
26	chr4:54001200-54009800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:54001200-54017600	Weak transcription	Spleen	Spleen
28	chr4:54002600-54009800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr4:54003400-54019000	Weak transcription	GM12878-XiMat	blood
30	chr4:54003600-54012800	Weak transcription	Esophagus	oesophagus
31	chr4:54004000-54017600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:54004200-54011000	Weak transcription	Pancreas	Pancrea
33	chr4:54004200-54020800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:54004200-54052200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:54005400-54010800	Weak transcription	Dnd41	blood
36	chr4:54005400-54012400	Weak transcription	HMEC	breast
37	chr4:54005600-54023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr4:54005800-54012800	Weak transcription	Fetal Brain Female	brain
39	chr4:54006200-54010200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr4:54006400-54010200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:54006600-54011000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr4:54006600-54011000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:54006600-54011000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr4:54006800-54010800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr4:54007000-54017600	Weak transcription	Right Ventricle	heart
46	chr4:54007200-54030600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:54007600-54010000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:54008000-54010800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr4:54008000-54011600	Strong transcription	Primary B cells from cord blood	blood
50	chr4:54008200-54009600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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