Variant report

Variant	rs6425606
Chromosome Location	chr1:180071987-180071988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179850618..179853198-chr1:180070366..180073320,2	K562	blood:

Variant related genes	Relation type
ENSG00000143337	Chromatin interaction
ENSG00000272906	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10913918	0.81[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs11810556	0.81[JPT][hapmap]
rs12075450	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs12091685	0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs12094391	0.86[ASN][1000 genomes]
rs1281384	0.85[JPT][hapmap]
rs1281389	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs17371566	0.83[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap]
rs1981314	0.85[JPT][hapmap]
rs2281805	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs2319676	0.88[CEU][hapmap];0.91[JPT][hapmap]
rs2319677	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2477106	0.90[ASW][hapmap];0.89[CEU][hapmap]
rs2477114	0.86[EUR][1000 genomes]
rs2477117	0.90[ASW][hapmap];0.89[CEU][hapmap];0.85[JPT][hapmap]
rs2483622	0.89[CEU][hapmap]
rs2501608	0.89[CEU][hapmap]
rs2777910	0.85[CHD][hapmap]
rs3767201	0.85[JPT][hapmap]
rs4147170	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4147171	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4263962	0.85[JPT][hapmap]
rs4379644	0.90[ASW][hapmap];0.89[CEU][hapmap];0.85[JPT][hapmap]
rs4604657	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4622030	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4651055	0.85[JPT][hapmap]
rs4652461	0.90[ASW][hapmap];0.84[CEU][hapmap]
rs4652470	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs504202	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs521858	0.85[JPT][hapmap]
rs526683	0.86[CEU][hapmap];0.84[JPT][hapmap]
rs533795	0.85[JPT][hapmap]
rs539324	0.85[EUR][1000 genomes]
rs551607	0.89[ASW][hapmap];0.88[CEU][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs552743	0.94[CEU][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs55953436	0.82[ASN][1000 genomes]
rs55971224	0.84[ASN][1000 genomes]
rs561233	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs56279106	0.81[ASN][1000 genomes]
rs585355	0.85[CHD][hapmap]
rs6425607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660984	0.85[JPT][hapmap]
rs6676989	0.90[ASW][hapmap];0.89[CEU][hapmap];0.85[JPT][hapmap]
rs6682558	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692394	0.85[JPT][hapmap]
rs7518534	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7521895	0.92[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7521948	0.90[ASW][hapmap];0.85[JPT][hapmap]
rs7545835	0.85[ASN][1000 genomes]
rs7547954	0.84[ASN][1000 genomes]
rs9425853	0.89[CEU][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv548344	chr1:179960787-180071987	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
9	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6425606	CEP350	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179970800-180076800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr1:179983600-180083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:180000800-180083400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:180002400-180085000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:180013000-180080000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:180029600-180084800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:180030000-180073000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:180040800-180082200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr1:180042000-180082600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:180044800-180077200	Weak transcription	Small Intestine	intestine
11	chr1:180048800-180082200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr1:180049000-180076800	Strong transcription	Primary B cells from cord blood	blood
13	chr1:180052800-180082600	Strong transcription	Fetal Thymus	thymus
14	chr1:180052800-180085800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:180053000-180072400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:180053000-180083000	Strong transcription	Liver	Liver
17	chr1:180053200-180072600	Strong transcription	Fetal Intestine Large	intestine
18	chr1:180054000-180082600	Strong transcription	Dnd41	blood
19	chr1:180054400-180072800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:180054600-180079400	Weak transcription	Fetal Brain Male	brain
21	chr1:180057600-180082600	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:180057600-180082800	Strong transcription	Adipose Nuclei	Adipose
23	chr1:180059000-180072600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr1:180059200-180073000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr1:180059200-180076000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:180059600-180073600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:180060000-180072800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:180060200-180072600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:180062600-180079600	Weak transcription	Fetal Heart	heart
30	chr1:180064400-180079400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:180065000-180078400	Weak transcription	Spleen	Spleen
32	chr1:180065000-180079400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:180065000-180079400	Weak transcription	Psoas Muscle	Psoas
34	chr1:180065000-180079400	Weak transcription	NHLF	lung
35	chr1:180065000-180080000	Weak transcription	NHEK	skin
36	chr1:180065000-180080200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:180065200-180078600	Weak transcription	Brain Angular Gyrus	brain
38	chr1:180065400-180080000	Weak transcription	HMEC	breast
39	chr1:180066200-180079400	Weak transcription	Colonic Mucosa	Colon
40	chr1:180066200-180079400	Weak transcription	Stomach Mucosa	stomach
41	chr1:180066200-180082200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:180066400-180075200	Weak transcription	HSMMtube	muscle
43	chr1:180066400-180077200	Weak transcription	Brain Substantia Nigra	brain
44	chr1:180066400-180079600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:180066400-180080000	Weak transcription	Brain Germinal Matrix	brain
46	chr1:180066400-180080200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:180066600-180079200	Weak transcription	NH-A	brain
48	chr1:180066600-180079400	Weak transcription	Brain Anterior Caudate	brain
49	chr1:180067200-180073600	Weak transcription	HepG2	liver
50	chr1:180067800-180077400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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