Variant report

Variant	rs4859889
Chromosome Location	chr4:78826021-78826022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78825966..78828608-chr4:78831298..78833408,2	K562	blood:
2	chr4:78819042..78822002-chr4:78825525..78828218,2	K562	blood:
3	chr4:78817939..78819468-chr4:78825974..78827657,2	MCF-7	breast:
4	chr17:58231868..58233857-chr4:78823862..78826413,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10033527	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10033613	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1021824	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1021826	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11097938	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11729215	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs12645742	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13101418	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13101987	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap]
rs13103035	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.83[ASN][1000 genomes]
rs13103523	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13104947	0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap]
rs13106067	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13119606	0.85[ASN][1000 genomes]
rs13120272	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16996915	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.84[ASN][1000 genomes]
rs17002849	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2088992	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs2134050	0.88[ASN][1000 genomes]
rs28404443	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28855210	0.88[ASN][1000 genomes]
rs34830788	0.82[ASN][1000 genomes]
rs35648590	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35735677	0.86[ASN][1000 genomes]
rs35979107	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4453957	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4571357	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4577601	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4859509	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859511	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859877	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[MKK][hapmap]
rs4859879	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.85[ASN][1000 genomes]
rs4859888	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62302728	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62302732	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6533282	0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6533291	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6533344	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533345	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66825464	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6811736	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6814912	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6848029	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6854895	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7670157	0.82[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7675009	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7676660	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7698627	0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7698629	0.83[EUR][1000 genomes]
rs905376	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised 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	12 gene(s)	inside rSNPs	diseases
2	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4859889	C4orf26	cis	parietal	SCAN
rs4859889	MRPL1	cis	cerebellum	SCAN
rs4859889	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs4859889	MRPL1	cis	multi-tissue	Pritchard
rs4859889	MRPL1	cis	lymphoblastoid	seeQTL
rs4859889	FRAS1	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78784800-78842200	Weak transcription	HSMMtube	muscle
2	chr4:78784800-78859800	Weak transcription	Esophagus	oesophagus
3	chr4:78785000-78831200	Weak transcription	Brain Angular Gyrus	brain
4	chr4:78785000-78831600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr4:78785000-78841800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
7	chr4:78785400-78829800	Weak transcription	Fetal Heart	heart
8	chr4:78790600-78843400	Weak transcription	Small Intestine	intestine
9	chr4:78794000-78851200	Weak transcription	Spleen	Spleen
10	chr4:78794200-78851800	Weak transcription	Lung	lung
11	chr4:78795600-78831800	Weak transcription	NHLF	lung
12	chr4:78795600-78833000	Weak transcription	Brain Germinal Matrix	brain
13	chr4:78799200-78832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:78802400-78858400	Weak transcription	Aorta	Aorta
15	chr4:78806000-78841400	Weak transcription	A549	lung
16	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:78806600-78875600	Weak transcription	Colonic Mucosa	Colon
18	chr4:78808800-78852400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:78809200-78836800	Weak transcription	Fetal Brain Female	brain
20	chr4:78809200-78837400	Weak transcription	Fetal Brain Male	brain
21	chr4:78809200-78847000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:78809400-78829800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:78809400-78831000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:78809400-78831200	Weak transcription	Brain Substantia Nigra	brain
25	chr4:78809400-78831600	Weak transcription	Brain Anterior Caudate	brain
26	chr4:78809400-78834400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:78809400-78841000	Weak transcription	Hela-S3	cervix
28	chr4:78809600-78851200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:78809600-78851400	Weak transcription	Ovary	ovary
30	chr4:78809600-78865400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:78809600-78881200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:78810000-78829800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:78810000-78851800	Weak transcription	Thymus	Thymus
34	chr4:78810400-78843400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:78814000-78841600	Weak transcription	Osteobl	bone
36	chr4:78814400-78829600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:78814600-78828600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:78814600-78829000	Weak transcription	Fetal Intestine Large	intestine
39	chr4:78814600-78829800	Weak transcription	Fetal Stomach	stomach
40	chr4:78814600-78829800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr4:78814600-78843400	Weak transcription	Left Ventricle	heart
42	chr4:78814600-78874400	Weak transcription	Pancreas	Pancrea
43	chr4:78816400-78829800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:78816400-78833200	Weak transcription	HUVEC	blood vessel
45	chr4:78816400-78866400	Weak transcription	Fetal Thymus	thymus
46	chr4:78816400-78876000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:78816600-78829000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:78816600-78851400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:78816600-78875800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr4:78818600-78831600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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