Variant report

Variant	rs449077
Chromosome Location	chr7:107789927-107789928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107783148..107785666-chr7:107787857..107790630,2	MCF-7	breast:
2	chr7:107788123..107790344-chr7:107795941..107798117,2	K562	blood:
3	chr7:107789647..107791152-chr7:107794185..107796179,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs377348	0.90[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs377926	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs388557	0.81[CEU][hapmap];1.00[GIH][hapmap]
rs394921	0.84[GIH][hapmap]
rs413840	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs414077	0.90[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs435533	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs449506	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv831089	chr7:107687618-107877240	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs449077	LAMB4	cis	cerebellum	SCAN
rs449077	ATG12	trans	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107783000-107792600	Weak transcription	Pancreas	Pancrea
2	chr7:107786800-107790400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:107786800-107790400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr7:107786800-107798000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:107786800-107805600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:107786800-107811800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:107786800-107818400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:107786800-107819000	Weak transcription	Brain Angular Gyrus	brain
9	chr7:107786800-107857800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:107787000-107793000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:107787000-107818800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:107787400-107790600	Strong transcription	A549	lung
13	chr7:107787600-107799600	Weak transcription	Placenta	Placenta
14	chr7:107787600-107799800	Weak transcription	Fetal Brain Female	brain
15	chr7:107787600-107818800	Weak transcription	Brain Anterior Caudate	brain
16	chr7:107787800-107800400	Weak transcription	Fetal Muscle Leg	muscle
17	chr7:107787800-107807800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:107787800-107844200	Weak transcription	Brain Germinal Matrix	brain
19	chr7:107788000-107791600	Weak transcription	Liver	Liver
20	chr7:107788000-107798400	Weak transcription	Fetal Intestine Large	intestine
21	chr7:107788800-107796000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr7:107789000-107790800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:107789200-107790400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:107789200-107791000	Strong transcription	HUVEC	blood vessel
25	chr7:107789400-107790600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:107789400-107790600	Enhancers	NHLF	lung
27	chr7:107789400-107790800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:107789600-107790200	Enhancers	Rectal Smooth Muscle	rectum
29	chr7:107789600-107790600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:107789600-107790800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr7:107789600-107791000	Enhancers	Fetal Lung	lung
32	chr7:107789800-107790000	Enhancers	Stomach Smooth Muscle	stomach

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