Variant report

Variant	rs3001857
Chromosome Location	chr10:52419282-52419283
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	chr10:52414539..52416441-chr10:52417401..52419945,2	MCF-7	breast:
2	chr10:52381243..52386496-chr10:52418227..52421959,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000231345	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13376734	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001853	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001855	0.97[EUR][1000 genomes]
rs3001856	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001858	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3001859	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001860	0.86[EUR][1000 genomes]
rs3001861	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3001864	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3001865	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3001866	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001867	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001884	0.94[EUR][1000 genomes]
rs3011717	0.88[EUR][1000 genomes]
rs3011718	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011719	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3011728	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3011729	0.89[EUR][1000 genomes]
rs3011730	0.89[EUR][1000 genomes]
rs3011731	0.89[EUR][1000 genomes]
rs3011738	0.92[EUR][1000 genomes]
rs3011739	0.87[EUR][1000 genomes]
rs3011740	0.81[EUR][1000 genomes]
rs3011748	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3011752	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56153288	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56266445	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57025029	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67094247	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7067608	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7074349	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7077555	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7077589	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7078586	0.94[EUR][1000 genomes]
rs7096920	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7100589	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72787008	0.90[EUR][1000 genomes]
rs72803755	0.94[EUR][1000 genomes]
rs7897345	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7904446	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7908093	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv895393	chr10:52413720-52530819	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv948007	chr10:52414948-52500270	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv8662	chr10:52416662-52461079	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52413600-52419600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr10:52413600-52419600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:52414000-52419600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr10:52414000-52419600	Weak transcription	Primary T cells from cord blood	blood
5	chr10:52414000-52419800	Weak transcription	HUVEC	blood vessel
6	chr10:52414400-52419600	Weak transcription	Placenta	Placenta
7	chr10:52414600-52419600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr10:52417400-52419400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr10:52417600-52420200	Active TSS	K562	blood
10	chr10:52418200-52419600	Weak transcription	Pancreas	Pancrea
11	chr10:52418600-52419400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr10:52418600-52419400	Enhancers	Fetal Intestine Large	intestine
13	chr10:52418800-52419400	Enhancers	Liver	Liver
14	chr10:52418800-52419400	Weak transcription	Fetal Stomach	stomach
15	chr10:52418800-52419400	Enhancers	Stomach Mucosa	stomach
16	chr10:52419000-52419600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr10:52419000-52419600	Flanking Active TSS	GM12878-XiMat	blood
18	chr10:52419000-52420000	Strong transcription	Right Atrium	heart
19	chr10:52419000-52420400	Active TSS	Hela-S3	cervix
20	chr10:52419200-52419400	Enhancers	Primary B cells from peripheral blood	blood
21	chr10:52419200-52419400	Enhancers	Primary T cells fromperipheralblood	blood
22	chr10:52419200-52419400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr10:52419200-52419400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr10:52419200-52419400	Active TSS	Fetal Thymus	thymus
25	chr10:52419200-52419400	Enhancers	Thymus	Thymus
26	chr10:52419200-52419600	Enhancers	Primary B cells from cord blood	blood
27	chr10:52419200-52419800	Flanking Active TSS	HepG2	liver
28	chr10:52419200-52420000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr10:52419200-52420200	Active TSS	Fetal Intestine Small	intestine
30	chr10:52419200-52420400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr10:52419200-52420400	Active TSS	A549	lung

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