Variant report

Variant	rs6447666
Chromosome Location	chr4:48879374-48879375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48832600..48834706-chr4:48878011..48879626,2	K562	blood:
2	chr4:48780562..48783148-chr4:48877273..48880110,3	MCF-7	breast:
3	chr4:48833159..48834706-chr4:48878126..48880234,3	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction
ENSG00000109180	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10049761	0.81[GIH][hapmap]
rs11727343	0.90[GIH][hapmap];0.86[TSI][hapmap]
rs11729065	0.83[EUR][1000 genomes]
rs11733534	0.84[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs11734191	0.84[EUR][1000 genomes]
rs13142540	0.85[YRI][hapmap]
rs13149083	0.84[GIH][hapmap]
rs13152270	0.85[EUR][1000 genomes]
rs1554256	0.81[GIH][hapmap]
rs2085292	0.92[CEU][hapmap];0.81[GIH][hapmap]
rs2290516	0.81[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap]
rs2572345	0.90[GIH][hapmap];0.82[TSI][hapmap]
rs2572350	0.86[GIH][hapmap]
rs2605267	0.84[CEU][hapmap]
rs2712156	0.90[GIH][hapmap];0.82[TSI][hapmap]
rs2712158	0.88[GIH][hapmap]
rs3761729	0.88[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs4695407	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs7660206	0.81[GIH][hapmap];0.81[YRI][hapmap]
rs7665209	0.86[GIH][hapmap]
rs7687992	0.87[EUR][1000 genomes]
rs9291326	0.88[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs9637562	0.83[EUR][1000 genomes]
rs9997920	0.88[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
14	esv3692819	chr4:48875926-48887608	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6447666	MGC45416	cis	multi-tissue	Pritchard
rs6447666	SLC10A4	cis	lung	GTEx
rs6447666	OCIAD1	cis	brain	BrainEAC

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48848200-48880000	Weak transcription	Brain Substantia Nigra	brain
2	chr4:48860400-48882200	Weak transcription	Gastric	stomach
3	chr4:48860400-48901400	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:48860800-48892000	Weak transcription	Thymus	Thymus
5	chr4:48860800-48892800	Weak transcription	Aorta	Aorta
6	chr4:48860800-48892800	Weak transcription	Left Ventricle	heart
7	chr4:48860800-48895000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:48860800-48895000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:48863600-48892000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr4:48873200-48892000	Weak transcription	Primary T cells from cord blood	blood
11	chr4:48874000-48893600	Weak transcription	Pancreas	Pancrea
12	chr4:48875000-48892000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:48877400-48891800	Weak transcription	Fetal Brain Female	brain
14	chr4:48877800-48897000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:48878800-48879600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:48879000-48880600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:48879000-48880600	Enhancers	NHEK	skin
18	chr4:48879200-48879400	Enhancers	Right Ventricle	heart
19	chr4:48879200-48880400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:48879200-48880600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:48879200-48880600	Enhancers	HMEC	breast

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