Variant report

Variant	rs4396679
Chromosome Location	chr2:189190704-189190705
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:189155671..189159103-chr2:189189018..189193192,5	K562	blood:
2	chr2:189167037..189169913-chr2:189190017..189191810,2	K562	blood:
3	chr2:189157075..189159103-chr2:189189922..189191822,3	K562	blood:
4	chr2:189182622..189184644-chr2:189189029..189191672,2	K562	blood:
5	chr2:189186452..189188771-chr2:189190439..189192055,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144366	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10193506	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10197499	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10197505	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10804020	0.80[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10931346	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10931359	0.81[CEU][hapmap]
rs11687248	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs11689976	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12465164	0.82[CEU][hapmap]
rs12465625	0.81[CEU][hapmap]
rs12469904	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13008931	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13014693	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13022513	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13429603	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs34445909	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35964306	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4294965	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4402720	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4413123	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4426503	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4516391	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4591312	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4599076	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4610010	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4667215	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6712056	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6724428	1.00[JPT][hapmap]
rs6724636	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6744629	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6753371	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7425596	0.84[EUR][1000 genomes]
rs7564706	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7566619	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7586390	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7593546	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][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	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv431890	chr2:189175905-189202876	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1010330	chr2:189182307-189265614	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv584053	chr2:189184422-189245515	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv999135	chr2:189184937-189265614	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv584054	chr2:189185726-189233419	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4396679	GULP1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189178400-189191400	Weak transcription	Fetal Lung	lung
2	chr2:189182000-189191400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:189182000-189192200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:189183000-189196000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr2:189183400-189197200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:189183400-189198400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:189183600-189205000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:189183600-189205400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:189183800-189198600	Weak transcription	Ovary	ovary
10	chr2:189185000-189191600	Weak transcription	Placenta	Placenta
11	chr2:189187800-189191200	Weak transcription	Fetal Intestine Large	intestine
12	chr2:189187800-189204600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:189188000-189191200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:189188000-189191200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:189188000-189191200	Weak transcription	Stomach Mucosa	stomach
16	chr2:189188000-189191400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:189188000-189191400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:189188000-189191600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:189188000-189191600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:189188200-189191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:189188200-189191400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:189188200-189191400	Weak transcription	Aorta	Aorta
23	chr2:189188200-189191600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:189188400-189191200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:189188800-189191400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:189188800-189210600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:189189000-189191200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:189189200-189191200	Weak transcription	A549	lung
29	chr2:189189200-189191600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr2:189189200-189198400	Weak transcription	HUVEC	blood vessel
31	chr2:189189600-189196000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr2:189189800-189190800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr2:189189800-189191400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:189189800-189191400	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:189189800-189191600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:189190000-189191400	Weak transcription	NHDF-Ad	bronchial
37	chr2:189190000-189192800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:189190200-189191200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:189190200-189191400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:189190200-189191400	Weak transcription	NHLF	lung
41	chr2:189190400-189191200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:189190400-189193400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:189190400-189194200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr2:189190600-189191000	Weak transcription	K562	blood
45	chr2:189190600-189191400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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