Variant report

Variant	rs16878638
Chromosome Location	chr6:87889675-87889676
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:87870688..87872534-chr6:87888705..87890644,2	K562	blood:
2	chr6:87884610..87889850-chr6:87890271..87893351,5	K562	blood:

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10488045	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10498960	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];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs16878473	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16878570	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];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878622	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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878712	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878713	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878729	0.91[EUR][1000 genomes]
rs16878734	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16878736	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16878809	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs16878856	0.88[EUR][1000 genomes]
rs16878863	0.88[EUR][1000 genomes]
rs16878942	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs16878991	0.95[YRI][hapmap]
rs16878999	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap]
rs16879012	0.95[YRI][hapmap]
rs1925693	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41273281	0.88[EUR][1000 genomes]
rs41273283	0.88[EUR][1000 genomes]
rs41397850	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];0.95[YRI][hapmap]
rs41398947	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs55647962	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs56096438	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56193950	0.88[EUR][1000 genomes]
rs56678817	0.88[EUR][1000 genomes]
rs56743579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56847789	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56947685	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56999910	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57043501	0.88[EUR][1000 genomes]
rs57116567	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57217108	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57421283	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57607342	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57962992	0.97[EUR][1000 genomes]
rs58032842	1.00[AMR][1000 genomes]
rs58124219	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58269367	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58327183	0.88[EUR][1000 genomes]
rs58474842	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58576901	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58731649	0.88[EUR][1000 genomes]
rs58735749	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58751410	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59034165	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59138817	0.88[EUR][1000 genomes]
rs59150116	0.88[EUR][1000 genomes]
rs59214037	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59344869	0.97[AFR][1000 genomes]
rs59495279	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59654654	0.87[EUR][1000 genomes]
rs59875769	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59964119	1.00[AMR][1000 genomes]
rs60074363	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60285195	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60544317	0.85[EUR][1000 genomes]
rs60746078	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60845773	0.88[EUR][1000 genomes]
rs60985818	0.94[EUR][1000 genomes]
rs60994855	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61047847	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61379368	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61705669	0.88[EUR][1000 genomes]
rs73483720	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483728	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483743	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483749	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483752	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483758	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483760	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483765	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483769	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483771	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73483774	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483790	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483796	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483799	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485808	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485811	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73485813	0.94[EUR][1000 genomes]
rs73485815	0.94[EUR][1000 genomes]
rs73485820	0.88[EUR][1000 genomes]
rs73485826	0.88[EUR][1000 genomes]
rs73485828	0.88[EUR][1000 genomes]
rs73485831	0.88[EUR][1000 genomes]
rs73485848	0.88[EUR][1000 genomes]
rs73485849	0.88[EUR][1000 genomes]
rs73499768	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73499770	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73499771	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73499800	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73499802	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501611	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73501620	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501623	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501629	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501632	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501636	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501638	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501641	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501658	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501662	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73751992	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv604114	chr6:87816905-87906053	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16878638	SEMA5A	trans	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87866600-87889800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:87866600-87890000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:87866600-87890200	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:87867000-87895600	Weak transcription	HSMM	muscle
5	chr6:87867000-87915600	Weak transcription	NH-A	brain
6	chr6:87867200-87893400	Weak transcription	Adipose Nuclei	Adipose
7	chr6:87868000-87933000	Weak transcription	Hela-S3	cervix
8	chr6:87868600-87889800	Weak transcription	Fetal Intestine Large	intestine
9	chr6:87871400-87890000	Weak transcription	Pancreas	Pancrea
10	chr6:87871400-87890200	Weak transcription	Gastric	stomach
11	chr6:87874200-87890000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:87874200-87892600	Weak transcription	NHDF-Ad	bronchial
13	chr6:87874400-87924200	Weak transcription	Fetal Kidney	kidney
14	chr6:87874600-87890000	Weak transcription	Psoas Muscle	Psoas
15	chr6:87875000-87910400	Weak transcription	K562	blood
16	chr6:87876400-87890200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:87876400-87890600	Weak transcription	NHLF	lung
18	chr6:87876600-87890000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:87879800-87889800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:87879800-87889800	Weak transcription	Fetal Intestine Small	intestine
21	chr6:87879800-87890000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:87879800-87890000	Weak transcription	Lung	lung
23	chr6:87879800-87923000	Weak transcription	Esophagus	oesophagus
24	chr6:87880200-87893000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:87880600-87906000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:87881200-87893400	Weak transcription	HepG2	liver
27	chr6:87881400-87926200	Weak transcription	Liver	Liver
28	chr6:87881600-87893000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:87881600-87893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:87881800-87909400	Weak transcription	Fetal Brain Male	brain
31	chr6:87882000-87899400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:87882200-87889800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr6:87882200-87889800	Weak transcription	Ovary	ovary
34	chr6:87882200-87890000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr6:87882200-87896400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:87882400-87889800	Weak transcription	Fetal Brain Female	brain
37	chr6:87883200-87890200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:87883400-87890200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:87883400-87926200	Weak transcription	Fetal Lung	lung
40	chr6:87883800-87893000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:87883800-87897600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:87884000-87889800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr6:87884000-87889800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr6:87884000-87890200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:87884000-87890200	Weak transcription	Right Ventricle	heart
46	chr6:87884000-87894000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:87884000-87894400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:87884000-87894600	Weak transcription	Small Intestine	intestine
49	chr6:87884000-87895200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:87884000-87895200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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