Variant report

Variant	rs2627828
Chromosome Location	chr4:143186491-143186492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10002140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10010617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10013734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10013826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10020099	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10026164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10027089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10027480	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10032526	0.92[GIH][hapmap]
rs1039133	1.00[CEU][hapmap]
rs1039134	0.88[AMR][1000 genomes]
rs10519631	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes]
rs10519633	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];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10519638	0.82[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12498546	0.85[GIH][hapmap]
rs12500835	0.85[TSI][hapmap]
rs12502271	1.00[CEU][hapmap]
rs12503726	1.00[CEU][hapmap]
rs1390992	0.84[ASN][1000 genomes]
rs1390993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1497142	0.94[ASN][1000 genomes]
rs1497143	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1497144	0.94[ASN][1000 genomes]
rs17015544	0.85[GIH][hapmap]
rs17015594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.94[ASN][1000 genomes]
rs17015598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17646885	0.88[AMR][1000 genomes]
rs17646914	0.88[AMR][1000 genomes]
rs17654944	0.86[ASW][hapmap];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];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1845974	0.94[ASN][1000 genomes]
rs1907110	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1907131	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1907132	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1907133	0.94[ASN][1000 genomes]
rs1907136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2055211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2270657	0.84[GIH][hapmap]
rs2276942	0.92[GIH][hapmap]
rs2322543	0.94[ASN][1000 genomes]
rs2627801	0.87[TSI][hapmap]
rs2627803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2627821	1.00[CEU][hapmap];0.94[ASN][1000 genomes]
rs2627825	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2627826	0.94[ASN][1000 genomes]
rs2627829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[ASN][1000 genomes]
rs2627830	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2627831	0.94[ASN][1000 genomes]
rs2636652	1.00[JPT][hapmap]
rs2636661	0.94[ASN][1000 genomes]
rs2636664	0.94[ASN][1000 genomes]
rs2636665	0.94[ASN][1000 genomes]
rs2636687	0.94[ASN][1000 genomes]
rs2636689	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2636690	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2645824	0.94[ASN][1000 genomes]
rs28602561	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3102442	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3104278	0.94[ASN][1000 genomes]
rs3104279	0.94[ASN][1000 genomes]
rs3775630	1.00[GIH][hapmap]
rs3775640	0.85[GIH][hapmap]
rs3775641	0.85[GIH][hapmap]
rs3775650	0.92[GIH][hapmap]
rs3775651	0.92[GIH][hapmap]
rs3775652	0.92[GIH][hapmap]
rs3775653	0.92[GIH][hapmap]
rs3775654	0.92[GIH][hapmap]
rs3775655	0.92[GIH][hapmap]
rs3775657	1.00[GIH][hapmap]
rs3775658	1.00[GIH][hapmap]
rs3775674	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4501295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[ASN][1000 genomes]
rs4574489	0.94[ASN][1000 genomes]
rs4956317	1.00[CEU][hapmap]
rs4956318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4956435	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs4956436	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4956437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs56044460	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66588504	0.94[ASN][1000 genomes]
rs66625631	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs67288745	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs67935763	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs68037727	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6816247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6842783	0.91[GIH][hapmap]
rs6845623	0.92[GIH][hapmap]
rs6850756	0.92[GIH][hapmap]
rs72718482	0.88[AMR][1000 genomes]
rs72718498	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72720404	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72720416	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72720418	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72722457	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72722463	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7697702	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs7699731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9308148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9986085	0.92[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	nsv595604	chr4:143077401-143228914	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2627828	EFCAB4A	trans	lymphoblastoid	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143174600-143190200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr4:143179800-143191000	Weak transcription	Colonic Mucosa	Colon
3	chr4:143181400-143187200	Weak transcription	Right Ventricle	heart
4	chr4:143181400-143191400	Weak transcription	Left Ventricle	heart
5	chr4:143181600-143195600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:143183000-143204800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:143183400-143189600	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr4:143183600-143189200	Enhancers	Fetal Heart	heart
9	chr4:143184200-143189000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:143184200-143189400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:143184400-143186800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:143184400-143187200	Weak transcription	Pancreas	Pancrea
13	chr4:143184800-143189000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr4:143185000-143187400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr4:143185000-143187400	Enhancers	Hela-S3	cervix
16	chr4:143185000-143187600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr4:143185000-143188600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:143185400-143187000	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr4:143185400-143192400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:143185400-143199000	Weak transcription	Psoas Muscle	Psoas
21	chr4:143185600-143186800	Weak transcription	Small Intestine	intestine
22	chr4:143185600-143187200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:143185600-143187400	Enhancers	NHDF-Ad	bronchial
24	chr4:143185600-143188000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr4:143185800-143187800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr4:143186000-143186600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr4:143186000-143187400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:143186000-143187400	Enhancers	Primary T cells fromperipheralblood	blood
29	chr4:143186000-143187400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:143186000-143187400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr4:143186000-143187400	Enhancers	Fetal Muscle Leg	muscle
32	chr4:143186000-143187400	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr4:143186000-143187400	Enhancers	Stomach Mucosa	stomach
34	chr4:143186000-143187400	Enhancers	Dnd41	blood
35	chr4:143186000-143187400	Enhancers	HUVEC	blood vessel
36	chr4:143186000-143187400	Enhancers	NH-A	brain
37	chr4:143186000-143187600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:143186000-143187600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr4:143186000-143188800	Enhancers	HSMMtube	muscle
40	chr4:143186200-143186600	Genic enhancers	Primary T cells from cord blood	blood
41	chr4:143186200-143186600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:143186200-143186600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr4:143186200-143186600	Enhancers	NHLF	lung
44	chr4:143186200-143186800	Active TSS	Aorta	Aorta
45	chr4:143186200-143187000	Flanking Active TSS	A549	lung
46	chr4:143186200-143187400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:143186200-143187400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:143186200-143187400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:143186200-143187400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:143186200-143187600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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