Variant report

Variant	rs6428402
Chromosome Location	chr1:197440280-197440281
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	chr1:197439603..197440481-chr1:197454792..197455642,4	MCF-7	breast:
2	chr1:197434277..197436893-chr1:197438363..197440563,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1022908	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1033826	1.00[AMR][1000 genomes]
rs10494753	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10801606	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10922235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12089070	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1421390	1.00[AMR][1000 genomes]
rs1421391	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1421394	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1570412	1.00[AMR][1000 genomes]
rs1570413	1.00[AMR][1000 genomes]
rs1592707	1.00[AMR][1000 genomes]
rs1592708	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1923758	1.00[AMR][1000 genomes]
rs1951697	0.85[AMR][1000 genomes]
rs1998433	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2146484	0.87[AMR][1000 genomes]
rs2146485	1.00[AMR][1000 genomes]
rs2160967	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2160968	1.00[ASN][1000 genomes]
rs2181373	1.00[AMR][1000 genomes]
rs2359119	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2821099	1.00[AMR][1000 genomes]
rs3888104	1.00[AMR][1000 genomes]
rs3902057	1.00[AMR][1000 genomes]
rs4244150	0.87[AMR][1000 genomes]
rs4335404	1.00[AMR][1000 genomes]
rs4428919	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4989560	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6428401	0.87[AMR][1000 genomes]
rs6428403	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6428405	1.00[AMR][1000 genomes]
rs6428406	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6656674	1.00[AMR][1000 genomes]
rs6664766	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6670147	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6678776	0.87[AMR][1000 genomes]
rs6684593	1.00[AMR][1000 genomes]
rs6686241	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6689739	1.00[AMR][1000 genomes]
rs6690015	0.87[AMR][1000 genomes]
rs6691940	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6694254	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73073604	1.00[ASN][1000 genomes]
rs7514167	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7515671	1.00[ASN][1000 genomes]
rs7515749	1.00[AMR][1000 genomes]
rs7525737	0.87[AMR][1000 genomes]
rs7530158	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs927511	1.00[AMR][1000 genomes]
rs942050	0.87[AMR][1000 genomes]
rs980370	1.00[AMR][1000 genomes]
rs980371	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	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197435200-197440800	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr1:197435800-197440800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:197436600-197440600	Enhancers	Primary hematopoietic stem cells	blood
4	chr1:197437800-197441400	Weak transcription	Fetal Intestine Large	intestine
5	chr1:197438000-197440600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:197438600-197440400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr1:197438600-197440600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:197438600-197441000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr1:197438600-197441200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr1:197438600-197441800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr1:197438800-197440400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:197438800-197441200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:197438800-197441400	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr1:197438800-197442000	Enhancers	Ovary	ovary
15	chr1:197439000-197440400	Enhancers	Brain Germinal Matrix	brain
16	chr1:197439000-197440800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:197439000-197440800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:197439000-197440800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr1:197439000-197440800	Enhancers	Brain Anterior Caudate	brain
20	chr1:197439000-197441000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:197439000-197441400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:197439000-197442000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:197439000-197442400	Enhancers	Fetal Brain Male	brain
24	chr1:197439000-197442600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:197439200-197440400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:197439200-197440800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:197439400-197440400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:197439600-197440800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:197439600-197440800	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr1:197439800-197440600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:197439800-197441200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:197440000-197440400	Enhancers	Fetal Brain Female	brain
33	chr1:197440000-197440800	Enhancers	Brain Hippocampus Middle	brain
34	chr1:197440200-197440800	Enhancers	Brain Substantia Nigra	brain
35	chr1:197440200-197440800	Enhancers	Fetal Muscle Trunk	muscle
36	chr1:197440200-197440800	Enhancers	Fetal Muscle Leg	muscle
37	chr1:197440200-197441400	Enhancers	Fetal Lung	lung

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