Variant report

Variant	rs6429606
Chromosome Location	chr1:47062900-47062901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47058514..47060124-chr1:47061743..47063610,2	MCF-7	breast:
2	chr1:47054104..47055847-chr1:47061988..47063605,2	K562	blood:
3	chr1:47060645..47062314-chr1:47062417..47064887,3	K562	blood:
4	chr1:47052682..47056987-chr1:47061043..47065460,4	K562	blood:
5	chr1:47062611..47065175-chr1:47080228..47083086,2	MCF-7	breast:
6	chr1:47061375..47064454-chr1:47072882..47074737,3	K562	blood:

Variant related genes	Relation type
ENSG00000079277	Chromatin interaction
ENSG00000142961	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1054743	0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[ASN][1000 genomes]
rs10890405	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211306	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211309	0.94[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs11211312	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211317	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211328	0.95[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12029680	0.95[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12047046	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048342	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12093643	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12138971	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933934	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3753359	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766231	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766236	0.90[CHB][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766240	0.81[CHB][hapmap];0.84[TSI][hapmap]
rs3818323	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55680528	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56869893	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59446321	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552833	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556307	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556481	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764803	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8602	0.85[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs9659890	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9804164	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9804165	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1011892	chr1:47010519-47067492	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6429606	MKNK1	cis	cerebellum	SCAN
rs6429606	CLDN19	cis	cerebellum	SCAN
rs6429606	C1orf84	cis	cerebellum	SCAN
rs6429606	MKNK1	Cis_1M	lymphoblastoid	RTeQTL
rs6429606	C1orf223	cis	parietal	SCAN
rs6429606	MKNK1	cis	lung	GTEx
rs6429606	MOB3C	cis	Whole Blood	GTEx
rs6429606	MPL	cis	parietal	SCAN
rs6429606	RIMKLA	cis	parietal	SCAN
rs6429606	MKNK1	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47042600-47069000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:47042800-47068800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:47045600-47068800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:47046200-47069000	Weak transcription	Fetal Kidney	kidney
5	chr1:47048400-47069000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:47050600-47068600	Weak transcription	NHDF-Ad	bronchial
7	chr1:47055400-47068800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:47056400-47067000	Weak transcription	Stomach Mucosa	stomach
9	chr1:47056600-47068800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:47057000-47069000	Weak transcription	NH-A	brain
11	chr1:47057600-47065200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:47057600-47069000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:47058000-47068600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:47058600-47064800	Weak transcription	Brain Substantia Nigra	brain
15	chr1:47058600-47064800	Weak transcription	Small Intestine	intestine
16	chr1:47058600-47065000	Weak transcription	Esophagus	oesophagus
17	chr1:47058600-47069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:47058800-47064400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:47058800-47064600	Weak transcription	Psoas Muscle	Psoas
20	chr1:47058800-47065600	Weak transcription	NHLF	lung
21	chr1:47058800-47068600	Weak transcription	Fetal Lung	lung
22	chr1:47058800-47068600	Weak transcription	Hela-S3	cervix
23	chr1:47059000-47064400	Weak transcription	Brain Angular Gyrus	brain
24	chr1:47059000-47064600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:47059000-47065000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:47059000-47065000	Weak transcription	Right Ventricle	heart
27	chr1:47059000-47065200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:47059000-47068400	Weak transcription	Aorta	Aorta
29	chr1:47059000-47068800	Weak transcription	Ovary	ovary
30	chr1:47059000-47068800	Weak transcription	HUVEC	blood vessel
31	chr1:47059200-47063000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr1:47059200-47064400	Weak transcription	Brain Germinal Matrix	brain
33	chr1:47059200-47065000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:47059200-47067000	Weak transcription	HepG2	liver
35	chr1:47059200-47067400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:47059200-47068600	Weak transcription	Colonic Mucosa	Colon
37	chr1:47059200-47068600	Weak transcription	Fetal Brain Female	brain
38	chr1:47059200-47068800	Weak transcription	A549	lung
39	chr1:47059600-47065200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:47059600-47068600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:47059800-47064000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:47059800-47067200	Weak transcription	Gastric	stomach
43	chr1:47059800-47067200	Weak transcription	HMEC	breast
44	chr1:47059800-47068600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:47059800-47068600	Weak transcription	Placenta	Placenta
46	chr1:47059800-47068800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:47059800-47068800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:47059800-47069000	Weak transcription	HSMMtube	muscle
49	chr1:47060000-47063000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:47060000-47063000	Weak transcription	Rectal Mucosa Donor 29	rectum

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