Variant report

Variant	rs4301600
Chromosome Location	chr1:179820793-179820794
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	chr1:179820647..179822358-chr1:179825151..179827760,2	K562	blood:
2	chr1:179818541..179821971-chr1:179834156..179837166,3	K562	blood:

Variant related genes	Relation type
ENSG00000258664	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1048418	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10494523	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10913893	1.00[CHB][hapmap]
rs10913894	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913895	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10913909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11590974	1.00[CHB][hapmap]
rs12119431	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12131200	1.00[CHD][hapmap]
rs12136091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12136465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12141134	1.00[CHD][hapmap]
rs12142457	1.00[CHB][hapmap]
rs12143942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12144346	1.00[CHD][hapmap]
rs12144352	1.00[CHD][hapmap]
rs12144991	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12723969	1.00[CHB][hapmap]
rs12756362	1.00[CHB][hapmap]
rs16854910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17370139	1.00[CHB][hapmap]
rs17371159	1.00[CHD][hapmap]
rs3845388	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61740391	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6425596	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6659939	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673144	1.00[CEU][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72708661	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72708662	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7518566	1.00[CHB][hapmap]
rs7527215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531195	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545581	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549317	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9726605	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	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
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers 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	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179795600-179834200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:179802400-179836200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:179803600-179833600	Weak transcription	Fetal Brain Male	brain
4	chr1:179807600-179827400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:179807800-179833800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:179808600-179822600	Strong transcription	Fetal Intestine Large	intestine
7	chr1:179808600-179837000	Strong transcription	Liver	Liver
8	chr1:179808600-179839800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:179808800-179836000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:179809200-179821600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:179809800-179827800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:179810200-179828000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:179812000-179822000	Strong transcription	Fetal Muscle Trunk	muscle
14	chr1:179812200-179827800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:179812600-179821800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:179812600-179842600	Weak transcription	Stomach Mucosa	stomach
17	chr1:179812800-179821000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:179812800-179821400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:179812800-179822000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:179812800-179822600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:179813000-179822000	Strong transcription	Adipose Nuclei	Adipose
22	chr1:179813000-179822600	Strong transcription	Placenta	Placenta
23	chr1:179813200-179821000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:179813200-179821000	Strong transcription	GM12878-XiMat	blood
25	chr1:179813200-179822000	Strong transcription	Primary B cells from peripheral blood	blood
26	chr1:179813200-179822000	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:179813200-179822200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:179813200-179822200	Strong transcription	Dnd41	blood
29	chr1:179813200-179822600	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:179813200-179823000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:179813200-179823400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:179813200-179839200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:179813400-179821000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:179813400-179821800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:179813400-179825400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr1:179813400-179834000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:179813600-179821000	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:179814000-179822000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr1:179814000-179822000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr1:179814000-179822000	Strong transcription	HUVEC	blood vessel
41	chr1:179814200-179821000	Strong transcription	NH-A	brain
42	chr1:179814200-179821200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:179814200-179823600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:179814200-179834400	Weak transcription	Fetal Heart	heart
45	chr1:179814400-179822200	Strong transcription	Osteobl	bone
46	chr1:179814400-179839200	Strong transcription	HSMM	muscle
47	chr1:179814600-179822200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:179814800-179821800	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:179815000-179821000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr1:179815000-179821200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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