Variant report

Variant	rs4689639
Chromosome Location	chr4:7213469-7213470
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7193967..7198194-chr4:7211180..7216303,6	MCF-7	breast:
2	chr4:7213265..7217793-chr4:7218088..7221480,5	MCF-7	breast:
3	chr4:7212723..7215466-chr4:7270786..7273618,2	MCF-7	breast:
4	chr4:7198471..7200046-chr4:7211779..7213963,2	MCF-7	breast:
5	chr4:7213111..7215832-chr4:7278141..7280454,2	MCF-7	breast:
6	chr4:7212738..7214685-chr4:7282671..7285326,2	MCF-7	breast:
7	chr4:7211941..7214123-chr4:7236956..7238612,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184985	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11722329	0.83[EUR][1000 genomes]
rs11727432	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11727443	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12509590	0.88[ASN][1000 genomes]
rs13121616	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1827297	0.83[AMR][1000 genomes]
rs4234797	0.81[MEX][hapmap];0.81[TSI][hapmap]
rs4234798	0.81[MEX][hapmap];0.81[TSI][hapmap]
rs4689085	0.84[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4689635	0.91[EUR][1000 genomes]
rs4689637	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4689640	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4689651	0.85[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs6852212	0.85[CHB][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv829850	chr4:7112509-7314016	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv461194	chr4:7154743-7219933	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv593561	chr4:7154743-7219933	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv432556	chr4:7174993-7391948	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv461197	chr4:7183984-7222362	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv593563	chr4:7183984-7222362	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv878540	chr4:7186257-7231782	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv593564	chr4:7197393-7222781	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv878541	chr4:7211197-7341243	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4689639	JAKMIP1	cis	cerebellum	SCAN
rs4689639	GPR78	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7207400-7214400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:7207400-7214600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:7209000-7214200	Enhancers	NH-A	brain
4	chr4:7209600-7215000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:7210000-7215800	Weak transcription	Right Atrium	heart
6	chr4:7210400-7222400	Weak transcription	Brain Anterior Caudate	brain
7	chr4:7210600-7214000	Weak transcription	Brain Substantia Nigra	brain
8	chr4:7210600-7214200	Enhancers	A549	lung
9	chr4:7210800-7218600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:7211000-7213800	Weak transcription	Esophagus	oesophagus
11	chr4:7211000-7213800	Enhancers	NHLF	lung
12	chr4:7211000-7214400	Weak transcription	Right Ventricle	heart
13	chr4:7211000-7216200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:7211200-7214400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:7211600-7214000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr4:7211600-7214200	Enhancers	HSMM	muscle
17	chr4:7211600-7214800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:7212400-7213800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:7212400-7215800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:7212600-7214400	Weak transcription	Lung	lung
21	chr4:7212600-7214600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:7212800-7213600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:7212800-7213800	Weak transcription	HMEC	breast
24	chr4:7212800-7215200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:7212800-7215200	Weak transcription	Fetal Stomach	stomach
26	chr4:7212800-7225400	Weak transcription	Ovary	ovary
27	chr4:7213200-7213600	Enhancers	Hela-S3	cervix
28	chr4:7213400-7214200	Enhancers	HSMMtube	muscle
29	chr4:7213400-7214600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:7213400-7215200	Enhancers	Liver	Liver

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