Variant report

Variant	rs3762288
Chromosome Location	chr1:10463572-10463573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10457481..10460919-chr1:10461476..10464361,6	MCF-7	breast:
2	chr1:10448039..10452372-chr1:10461454..10464650,4	MCF-7	breast:
3	chr1:10457799..10462480-chr1:10462835..10469512,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142657	Chromatin interaction
ENSG00000265945	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1002076	0.91[ASN][1000 genomes]
rs10864450	0.82[EUR][1000 genomes]
rs10864453	0.90[EUR][1000 genomes]
rs11121541	0.87[EUR][1000 genomes]
rs11121551	0.90[ASN][1000 genomes]
rs11121555	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11121557	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11121560	0.93[ASN][1000 genomes]
rs11121561	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11121563	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121566	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1138791	0.91[ASN][1000 genomes]
rs11576384	0.94[ASN][1000 genomes]
rs11579365	0.96[ASN][1000 genomes]
rs11585794	0.91[ASN][1000 genomes]
rs11586842	0.88[ASN][1000 genomes]
rs11587309	0.91[ASN][1000 genomes]
rs11587495	0.90[ASN][1000 genomes]
rs11587854	0.91[ASN][1000 genomes]
rs12118323	0.96[ASN][1000 genomes]
rs12128374	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12130563	0.80[ASN][1000 genomes]
rs12131441	0.80[ASN][1000 genomes]
rs12136404	0.80[EUR][1000 genomes]
rs12141201	0.91[ASN][1000 genomes]
rs12402723	0.92[EUR][1000 genomes]
rs12409754	0.91[ASN][1000 genomes]
rs12746471	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1467653	0.90[EUR][1000 genomes]
rs1536262	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17396973	0.80[EUR][1000 genomes]
rs17402762	0.90[EUR][1000 genomes]
rs2148152	0.80[ASN][1000 genomes]
rs2229687	0.96[ASN][1000 genomes]
rs2236678	0.96[ASN][1000 genomes]
rs34045426	0.93[ASN][1000 genomes]
rs34075302	0.89[ASN][1000 genomes]
rs35716098	0.96[ASN][1000 genomes]
rs35759975	0.96[ASN][1000 genomes]
rs35811280	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3737155	0.96[ASN][1000 genomes]
rs3748575	0.81[EUR][1000 genomes]
rs3748581	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762286	0.96[ASN][1000 genomes]
rs3762287	0.93[ASN][1000 genomes]
rs4845930	0.81[EUR][1000 genomes]
rs4846216	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4846218	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4846219	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846221	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58014725	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61778399	0.80[ASN][1000 genomes]
rs61778401	0.80[ASN][1000 genomes]
rs61778402	0.80[ASN][1000 genomes]
rs61778404	0.87[ASN][1000 genomes]
rs6541090	0.88[EUR][1000 genomes]
rs6541094	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674949	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6682868	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7546368	0.90[EUR][1000 genomes]
rs912962	0.83[EUR][1000 genomes]
rs9651117	0.93[ASN][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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS 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 target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3762288	PGD	Cis_1M	lymphoblastoid	RTeQTL
rs3762288	PGD	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10459600-10465000	Transcr. at gene 5' and 3'	A549	lung
2	chr1:10460000-10463800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:10460000-10490200	Weak transcription	Psoas Muscle	Psoas
4	chr1:10460200-10475400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:10460400-10463600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:10460400-10463800	Weak transcription	Gastric	stomach
7	chr1:10460400-10464200	Weak transcription	Pancreas	Pancrea
8	chr1:10460400-10464200	Weak transcription	Spleen	Spleen
9	chr1:10460400-10464800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:10460400-10472800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:10460400-10475200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:10460600-10463600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:10460600-10463800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:10460600-10464000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:10460600-10464200	Weak transcription	Small Intestine	intestine
16	chr1:10460600-10481200	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr1:10460800-10464200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:10460800-10468800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:10460800-10480400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:10460800-10482000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:10460800-10482400	Strong transcription	Fetal Stomach	stomach
22	chr1:10460800-10483400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:10461000-10464200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:10461000-10464600	Genic enhancers	HUVEC	blood vessel
25	chr1:10461000-10474600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:10461000-10475200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:10461000-10476800	Weak transcription	Fetal Heart	heart
28	chr1:10461000-10482000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:10461200-10463600	Weak transcription	Fetal Brain Male	brain
30	chr1:10461200-10464200	Genic enhancers	Hela-S3	cervix
31	chr1:10461200-10464400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:10461200-10464400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:10461200-10482000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:10461200-10482000	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:10461200-10490000	Weak transcription	Right Atrium	heart
36	chr1:10461400-10464400	Genic enhancers	NH-A	brain
37	chr1:10461400-10475200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:10461400-10483000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:10461400-10483000	Strong transcription	Fetal Intestine Small	intestine
40	chr1:10461400-10483400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr1:10461600-10463600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:10461600-10465200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:10461600-10481800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:10461600-10482800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:10461800-10465000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
46	chr1:10461800-10472800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr1:10461800-10473600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:10461800-10473600	Strong transcription	Primary hematopoietic stem cells	blood
49	chr1:10461800-10473600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:10461800-10473600	Strong transcription	Rectal Smooth Muscle	rectum

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