Variant report

Variant	rs6428344
Chromosome Location	chr1:196505869-196505870
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	chr1:196499979..196502866-chr1:196504435..196506284,2	MCF-7	breast:
2	chr1:196500682..196504253-chr1:196504889..196507898,3	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10737677	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10801540	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs10801541	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs10801542	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs10922080	0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1339948	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1339956	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1361402	1.00[YRI][hapmap]
rs1416963	1.00[AMR][1000 genomes]
rs1416968	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1416969	1.00[YRI][hapmap]
rs1538681	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1538682	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16839769	1.00[AMR][1000 genomes]
rs16839916	1.00[AMR][1000 genomes]
rs16840189	1.00[AMR][1000 genomes]
rs16840219	1.00[AMR][1000 genomes]
rs1890801	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2335902	1.00[AMR][1000 genomes]
rs2335904	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4255328	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4290012	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4411090	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4484881	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4500252	1.00[AMR][1000 genomes]
rs4607811	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4658035	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4658037	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4658038	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4658044	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4658045	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60840993	1.00[AMR][1000 genomes]
rs6413932	1.00[AMR][1000 genomes]
rs6413933	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs6428343	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6428345	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6657157	1.00[AMR][1000 genomes]
rs6664020	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6678139	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6679424	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6690518	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6690846	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6692565	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6698581	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73065832	1.00[AMR][1000 genomes]
rs73065849	1.00[AMR][1000 genomes]
rs7511869	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7512647	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7527233	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7544266	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7552572	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs946754	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1009233	chr1:196301712-196568874	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196503600-196509600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr1:196503800-196509800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
3	chr1:196504200-196508000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
4	chr1:196504200-196508000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
5	chr1:196504200-196508000	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
6	chr1:196504400-196506800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
7	chr1:196504800-196506400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:196504800-196506600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:196504800-196506800	ZNF genes & repeats	Fetal Lung	lung
10	chr1:196504800-196507000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
11	chr1:196504800-196507800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:196504800-196508000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:196505000-196507000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:196505000-196507800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:196505200-196507000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
16	chr1:196505200-196507200	ZNF genes & repeats	Fetal Muscle Leg	muscle
17	chr1:196505200-196507400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:196505400-196506800	Strong transcription	Liver	Liver
19	chr1:196505400-196507400	ZNF genes & repeats	Fetal Stomach	stomach
20	chr1:196505600-196506600	ZNF genes & repeats	Brain Germinal Matrix	brain
21	chr1:196505800-196507800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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