Variant report

Variant	rs4689860
Chromosome Location	chr4:7778663-7778664
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	chr4:7769826..7772813-chr4:7778014..7779534,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10009045	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10018256	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10049998	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs11932843	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs12639946	0.89[CEU][hapmap]
rs13131154	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs13140004	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs17770147	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs17770177	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs2067842	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2385902	0.86[CHB][hapmap]
rs2891927	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs3934540	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4234831	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4256209	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs4296663	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs4361385	0.84[JPT][hapmap]
rs4411970	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs4443285	0.94[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4447865	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4487321	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs4579115	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4689865	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689875	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4696742	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs4696772	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs6446624	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6446625	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6446627	0.80[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs6446629	0.80[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs6824266	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs6828574	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs6828858	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6829710	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6832352	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs6833054	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs6845014	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs6856371	0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6856795	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71612280	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7654361	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7682202	0.80[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7682611	0.89[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs7684718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7697255	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9996019	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][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	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4689860	MSX1	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7757600-7779600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr4:7758000-7780800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:7758200-7783200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
5	chr4:7758600-7780600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:7759400-7790400	Weak transcription	Psoas Muscle	Psoas
7	chr4:7760000-7783000	Strong transcription	HSMMtube	muscle
8	chr4:7760000-7783200	Strong transcription	HSMM	muscle
9	chr4:7760200-7779400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:7760400-7780400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:7760600-7780000	Weak transcription	Right Atrium	heart
12	chr4:7761000-7780400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:7761200-7781000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:7761400-7784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:7762000-7788000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
17	chr4:7765000-7780000	Strong transcription	Lung	lung
18	chr4:7766000-7780600	Strong transcription	Osteobl	bone
19	chr4:7766800-7781200	Strong transcription	HUVEC	blood vessel
20	chr4:7767200-7780800	Strong transcription	NH-A	brain
21	chr4:7767600-7781000	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr4:7769000-7780200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr4:7771600-7780800	Strong transcription	Pancreas	Pancrea
25	chr4:7771800-7780200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:7772000-7783000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr4:7772800-7778800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:7772800-7780400	Weak transcription	Brain Angular Gyrus	brain
29	chr4:7773600-7779000	Weak transcription	Primary T cells from cord blood	blood
30	chr4:7773600-7782800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:7773600-7783000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr4:7773600-7783600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr4:7773800-7779400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:7773800-7783400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:7774000-7782800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr4:7774000-7783400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr4:7774200-7781600	Strong transcription	A549	lung
38	chr4:7774400-7780600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:7774400-7781000	Weak transcription	Fetal Heart	heart
40	chr4:7774600-7780200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:7774600-7783000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:7774600-7783400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:7775000-7780600	Strong transcription	Adipose Nuclei	Adipose
44	chr4:7775200-7778800	Weak transcription	Fetal Kidney	kidney
45	chr4:7775200-7779400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:7775200-7779800	Strong transcription	NHLF	lung
47	chr4:7775200-7782400	Strong transcription	Placenta	Placenta
48	chr4:7775400-7779200	Enhancers	HepG2	liver
49	chr4:7775400-7780400	Strong transcription	Fetal Muscle Leg	muscle
50	chr4:7775400-7780800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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