Variant report

Variant	rs4956435
Chromosome Location	chr4:143062808-143062809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10002140	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10010617	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10013734	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs10013826	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10020099	0.87[EUR][1000 genomes]
rs10026164	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10027089	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10032526	0.91[GIH][hapmap]
rs1039132	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1039133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1039134	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519633	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs10519638	0.82[CEU][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap]
rs12498546	0.84[GIH][hapmap]
rs12500835	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12503726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12507662	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1390992	0.87[EUR][1000 genomes]
rs1390993	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs1497143	0.87[EUR][1000 genomes]
rs1497144	0.87[EUR][1000 genomes]
rs17015544	0.84[GIH][hapmap]
rs17015583	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015594	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17015598	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17646885	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17646914	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17654944	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs1874574	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1907110	0.82[CEU][hapmap]
rs1907123	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1907131	0.87[EUR][1000 genomes]
rs1907132	0.87[EUR][1000 genomes]
rs1907133	0.87[EUR][1000 genomes]
rs1907136	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2055211	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2270657	0.84[GIH][hapmap]
rs2276942	0.91[GIH][hapmap]
rs2322543	0.87[EUR][1000 genomes]
rs2627803	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2627805	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2627821	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2627825	0.87[EUR][1000 genomes]
rs2627826	0.87[EUR][1000 genomes]
rs2627828	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs2627829	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2627830	0.87[EUR][1000 genomes]
rs2627831	0.87[EUR][1000 genomes]
rs2636661	0.87[EUR][1000 genomes]
rs2636664	0.87[EUR][1000 genomes]
rs2636665	0.87[EUR][1000 genomes]
rs2636687	0.87[EUR][1000 genomes]
rs2636689	0.87[EUR][1000 genomes]
rs2636690	0.85[EUR][1000 genomes]
rs2645824	0.87[EUR][1000 genomes]
rs28602561	0.87[EUR][1000 genomes]
rs3104278	0.87[EUR][1000 genomes]
rs3104279	0.85[EUR][1000 genomes]
rs3775630	1.00[GIH][hapmap];0.88[TSI][hapmap]
rs3775640	0.84[GIH][hapmap]
rs3775641	0.84[GIH][hapmap]
rs3775650	0.91[GIH][hapmap]
rs3775651	0.91[GIH][hapmap]
rs3775652	0.91[GIH][hapmap]
rs3775653	0.91[GIH][hapmap]
rs3775654	0.91[GIH][hapmap]
rs3775655	0.91[GIH][hapmap]
rs3775657	1.00[GIH][hapmap]
rs3775658	1.00[GIH][hapmap]
rs3775674	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4501295	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs4574489	0.87[EUR][1000 genomes]
rs4956317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4956318	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4956436	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4956437	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs66532978	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66588504	0.87[EUR][1000 genomes]
rs66625631	0.90[EUR][1000 genomes]
rs67288745	0.90[EUR][1000 genomes]
rs67746056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67935763	0.87[EUR][1000 genomes]
rs68037727	0.87[EUR][1000 genomes]
rs6816247	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6842783	0.91[GIH][hapmap]
rs6845623	0.91[GIH][hapmap]
rs6850756	0.91[GIH][hapmap]
rs6852106	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72718464	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72718482	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72718498	0.87[EUR][1000 genomes]
rs72720404	0.85[EUR][1000 genomes]
rs72720416	0.87[EUR][1000 genomes]
rs72720418	0.87[EUR][1000 genomes]
rs7695458	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7697702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7699731	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9308148	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs9986085	0.91[GIH][hapmap]

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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830097	chr4:142949705-143136372	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv830098	chr4:143050143-143234384	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4956435	EFCAB4A	trans	lymphoblastoid	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143018800-143109600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:143025400-143066800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:143031000-143064800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:143043400-143089000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:143049800-143114400	Weak transcription	Right Ventricle	heart
6	chr4:143050000-143079600	Weak transcription	NHDF-Ad	bronchial
7	chr4:143050400-143063600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr4:143051400-143093400	Weak transcription	Left Ventricle	heart
9	chr4:143051800-143070600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:143052400-143081400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:143052400-143111600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:143052600-143081400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:143052600-143094600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:143054800-143065600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:143057600-143078800	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:143057800-143070200	Weak transcription	Fetal Heart	heart
17	chr4:143057800-143079000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:143057800-143114400	Weak transcription	Aorta	Aorta
19	chr4:143058000-143181000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:143059800-143063200	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:143059800-143068600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:143060400-143063600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:143060400-143072400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:143060800-143064200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:143061000-143063200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:143061000-143063600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:143061000-143081000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:143061200-143063600	Weak transcription	Dnd41	blood
29	chr4:143061200-143069400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:143061200-143079000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:143061200-143079200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:143061600-143063600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:143061600-143063600	Weak transcription	HSMM	muscle
34	chr4:143061800-143069200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:143061800-143102200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:143062200-143063600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr4:143062200-143063600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr4:143062200-143063600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr4:143062200-143063600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:143062200-143065000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr4:143062200-143066000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr4:143062200-143066200	Weak transcription	Primary T cells from cord blood	blood
43	chr4:143062200-143068800	Weak transcription	HSMMtube	muscle
44	chr4:143062200-143081200	Weak transcription	NHEK	skin
45	chr4:143062400-143063800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:143062400-143066400	Weak transcription	HMEC	breast
47	chr4:143062600-143063400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr4:143062800-143064000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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