Variant report

Variant	rs6442108
Chromosome Location	chr3:48192959-48192960
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47873536..47875559-chr3:48191736..48194650,2	MCF-7	breast:
2	chr3:47462491..47463126-chr3:48192708..48193228,2	K562	blood:
3	chr3:47865781..47868282-chr3:48191820..48194730,2	K562	blood:
4	chr3:48191366..48194306-chr3:48197908..48200295,2	K562	blood:
5	chr3:47879327..47879852-chr3:48192756..48193326,2	K562	blood:
6	chr3:47911284..47912012-chr3:48192739..48193284,2	MCF-7	breast:
7	chr3:47878930..47879447-chr3:48192753..48193491,3	MCF-7	breast:
8	chr3:47866336..47866964-chr3:48192656..48193221,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000114650	Chromatin interaction
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11130157	0.88[EUR][1000 genomes]
rs11711766	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493256	0.96[EUR][1000 genomes]
rs12494304	0.96[EUR][1000 genomes]
rs12494396	0.91[EUR][1000 genomes]
rs12495221	0.97[EUR][1000 genomes]
rs12496784	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12633518	0.83[YRI][hapmap]
rs13099560	0.80[EUR][1000 genomes]
rs1380053	0.87[YRI][hapmap]
rs34422222	0.87[EUR][1000 genomes]
rs34513961	0.81[EUR][1000 genomes]
rs34648110	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35142214	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4858892	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62262998	0.88[EUR][1000 genomes]
rs62263001	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6442105	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6442106	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6442107	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442110	0.81[CEU][hapmap]
rs6766754	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6771787	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6771889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775114	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6796490	0.80[EUR][1000 genomes]
rs6797587	0.92[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6800730	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6806112	0.81[CEU][hapmap]
rs7374376	1.00[CEU][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes]
rs7429594	0.85[EUR][1000 genomes]
rs7431293	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7617773	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9822496	0.97[EUR][1000 genomes]
rs9832957	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases
7	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1012024	chr3:48119229-48242670	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs6442108	MRPS18AP1	cis	Nerve Tibial	GTEx
rs6442108	ZNF589	cis	Thyroid	GTEx
rs6442108	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs6442108	ZNF589	cis	Adipose Subcutaneous	GTEx
rs6442108	ZNF589	cis	Cerebellum	GTEx
rs6442108	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs6442108	CDC25A	cis	Thyroid	GTEx
rs6442108	ZNF589	cis	Temporal Cortex	GTEx
rs6442108	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs6442108	ZNF589	cis	Frontal Cortex	GTEx
rs6442108	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs6442108	CDC25A	cis	Muscle Skeletal	GTEx
rs6442108	MRPS18AP1	cis	Artery Tibial	GTEx
rs6442108	ZNF589	cis	lung	GTEx
rs6442108	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs6442108	ZNF589	cis	Artery Tibial	GTEx
rs6442108	MRPS18AP1	cis	lung	GTEx
rs6442108	CDC25A	cis	Adipose Subcutaneous	GTEx
rs6442108	MRPS18AP1	cis	Thyroid	GTEx
rs6442108	CDC25A	cis	Artery Tibial	GTEx
rs6442108	ZNF589	cis	Nerve Tibial	GTEx
rs6442108	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs6442108	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs6442108	ZNF589	cis	Brain Pons	GTEx
rs6442108	NME6	cis	Esophagus Muscularis	GTEx
rs6442108	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs6442108	MRPS18AP1	cis	Stomach	GTEx
rs6442108	ZNF589	cis	Esophagus Mucosa	GTEx
rs6442108	ZNF589	cis	Whole Blood	GTEx
rs6442108	NME6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48182200-48198400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:48182200-48199400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:48184200-48193000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:48184200-48196400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:48186000-48200200	Weak transcription	Spleen	Spleen
6	chr3:48191600-48194800	Enhancers	Fetal Muscle Trunk	muscle
7	chr3:48192000-48194000	Enhancers	NHLF	lung
8	chr3:48192200-48194000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:48192400-48193000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:48192400-48193000	Enhancers	Rectal Smooth Muscle	rectum
11	chr3:48192400-48193200	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr3:48192400-48193400	Enhancers	Colon Smooth Muscle	Colon
13	chr3:48192400-48193400	Enhancers	Fetal Stomach	stomach
14	chr3:48192400-48193600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:48192400-48193600	Enhancers	HUVEC	blood vessel
16	chr3:48192400-48194000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:48192400-48194000	Enhancers	Left Ventricle	heart
18	chr3:48192400-48194000	Enhancers	NHDF-Ad	bronchial
19	chr3:48192400-48194200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:48192400-48194200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:48192400-48194400	Enhancers	Fetal Muscle Leg	muscle
22	chr3:48192600-48193000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr3:48192600-48193000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr3:48192600-48193000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:48192600-48193000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr3:48192600-48193000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr3:48192600-48193000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:48192600-48193000	Enhancers	Brain Anterior Caudate	brain
29	chr3:48192600-48193000	Enhancers	Fetal Lung	lung
30	chr3:48192600-48193000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:48192600-48193000	Enhancers	NH-A	brain
32	chr3:48192600-48193200	Enhancers	Duodenum Mucosa	Duodenum
33	chr3:48192600-48193400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:48192600-48193400	Enhancers	Brain Cingulate Gyrus	brain
35	chr3:48192600-48193400	Enhancers	Stomach Smooth Muscle	stomach
36	chr3:48192600-48193600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:48192600-48193800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:48192600-48193800	Enhancers	Adipose Nuclei	Adipose
39	chr3:48192600-48193800	Enhancers	Colonic Mucosa	Colon
40	chr3:48192600-48193800	Enhancers	Fetal Intestine Large	intestine
41	chr3:48192600-48193800	Enhancers	Stomach Mucosa	stomach
42	chr3:48192600-48194000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:48192600-48194000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:48192600-48194000	Enhancers	Right Atrium	heart
45	chr3:48192600-48194000	Enhancers	Right Ventricle	heart
46	chr3:48192600-48194000	Flanking Active TSS	HepG2	liver
47	chr3:48192600-48194400	Enhancers	Fetal Heart	heart
48	chr3:48192600-48195000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:48192600-48200200	Weak transcription	Brain Germinal Matrix	brain
50	chr3:48192800-48193000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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