Variant report

Variant	rs4846218
Chromosome Location	chr1:10452040-10452041
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10447111..10452516-chr1:10455817..10460024,9	K562	blood:
2	chr1:10451777..10453446-chr1:10457951..10460281,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142657	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1002076	0.91[ASN][1000 genomes]
rs10864450	0.82[EUR][1000 genomes]
rs10864453	0.90[EUR][1000 genomes]
rs11121541	0.90[EUR][1000 genomes]
rs11121551	0.90[ASN][1000 genomes]
rs11121555	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11121557	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11121560	0.90[ASN][1000 genomes]
rs11121561	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11121563	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11121566	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1138791	0.91[ASN][1000 genomes]
rs11576384	0.83[ASN][1000 genomes]
rs11579365	0.84[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	0.84[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	0.81[EUR][1000 genomes]
rs12141201	0.91[ASN][1000 genomes]
rs12402723	0.91[EUR][1000 genomes]
rs12409754	0.91[ASN][1000 genomes]
rs12738317	0.80[ASN][1000 genomes]
rs12746471	0.87[ASN][1000 genomes]
rs1467653	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1536262	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17396973	0.81[EUR][1000 genomes]
rs17402762	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2148152	0.80[ASN][1000 genomes]
rs2229687	0.84[ASN][1000 genomes]
rs2236678	0.84[ASN][1000 genomes]
rs34045426	0.82[ASN][1000 genomes]
rs34075302	0.81[ASN][1000 genomes]
rs35716098	0.84[ASN][1000 genomes]
rs35759975	0.84[ASN][1000 genomes]
rs35811280	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3737155	0.87[ASN][1000 genomes]
rs3748575	0.82[EUR][1000 genomes]
rs3748579	0.80[ASN][1000 genomes]
rs3748581	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762286	0.84[ASN][1000 genomes]
rs3762287	0.82[ASN][1000 genomes]
rs3762288	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845930	0.81[EUR][1000 genomes]
rs4846216	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4846219	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4846221	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58014725	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[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	0.89[EUR][1000 genomes]
rs6541094	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6674949	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6682868	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7546368	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs912962	0.83[EUR][1000 genomes]
rs9651117	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv8213	chr1:10450914-10460439	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4846218	PGD	Cis_1M	lymphoblastoid	RTeQTL
rs4846218	PGD	cis	Muscle Skeletal	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10438600-10458200	Weak transcription	Right Atrium	heart
2	chr1:10439600-10458200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:10440000-10458400	Weak transcription	Lung	lung
4	chr1:10444800-10458200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:10445600-10454000	Weak transcription	Fetal Brain Female	brain
6	chr1:10447800-10454000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:10447800-10458400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:10448200-10452800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:10448200-10454200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:10448200-10458200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:10448200-10458200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:10448200-10458400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:10448400-10454400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:10448600-10453800	Weak transcription	Fetal Stomach	stomach
15	chr1:10448600-10454200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:10448600-10454800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:10448600-10458200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:10448600-10458200	Weak transcription	Brain Angular Gyrus	brain
19	chr1:10448600-10458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:10448600-10458400	Weak transcription	HSMM	muscle
21	chr1:10448800-10453400	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:10448800-10458200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:10448800-10458200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:10448800-10458200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:10448800-10458200	Weak transcription	HUVEC	blood vessel
26	chr1:10448800-10458200	Weak transcription	NH-A	brain
27	chr1:10448800-10458200	Weak transcription	NHEK	skin
28	chr1:10449000-10452600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:10449000-10453800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:10449000-10454000	Weak transcription	Brain Substantia Nigra	brain
31	chr1:10449000-10458200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:10449000-10458200	Weak transcription	Brain Anterior Caudate	brain
33	chr1:10449000-10458200	Weak transcription	Fetal Intestine Large	intestine
34	chr1:10449000-10458200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:10449000-10458200	Weak transcription	Thymus	Thymus
36	chr1:10449000-10458200	Weak transcription	HSMMtube	muscle
37	chr1:10449200-10458200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:10449200-10458200	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:10449200-10458400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:10449600-10454000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:10449600-10457400	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:10449600-10458200	Weak transcription	Esophagus	oesophagus
43	chr1:10449600-10458200	Weak transcription	Pancreas	Pancrea
44	chr1:10449600-10458200	Weak transcription	Hela-S3	cervix
45	chr1:10449800-10453800	Weak transcription	Fetal Intestine Small	intestine
46	chr1:10449800-10454000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:10450000-10454000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:10450000-10454400	Weak transcription	Brain Germinal Matrix	brain
49	chr1:10450200-10457200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:10450400-10452600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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