Variant report

Variant	rs661838
Chromosome Location	chr6:149628277-149628278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr6:149628138-149628436	MCF10A-Er-Src	breast:	n/a	chr6:149628262-149628270 chr6:149628266-149628273 chr6:149628264-149628273
2	SRF	chr6:149628186-149628370	GM12878	blood:	n/a	chr6:149628284-149628301
3	FOSL2	chr6:149628012-149628525	SK-N-SH	brain:	n/a	chr6:149628262-149628270 chr6:149628266-149628273 chr6:149628264-149628273
4	BATF	chr6:149628106-149628385	GM12878	blood:	n/a	chr6:149628265-149628276
5	FOS	chr6:149628098-149628410	MCF10A-Er-Src	breast:	n/a	chr6:149628262-149628270 chr6:149628266-149628273 chr6:149628264-149628273
6	TAF1	chr6:149628177-149628383	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr6:149628193-149628378	MCF10A-Er-Src	breast:	n/a	n/a
8	NR3C1	chr6:149628078-149628598	A549	lung:	n/a	chr6:149628381-149628395 chr6:149628380-149628395
9	FOS	chr6:149628093-149628419	MCF10A-Er-Src	breast:	n/a	chr6:149628262-149628270 chr6:149628266-149628273 chr6:149628264-149628273
10	NR3C1	chr6:149628204-149628450	A549	lung:	n/a	chr6:149628381-149628395 chr6:149628380-149628395
11	MYC	chr6:149628207-149628481	MCF10A-Er-Src	breast:	n/a	n/a
12	FOSL2	chr6:149628066-149628486	A549	lung:	n/a	chr6:149628262-149628270 chr6:149628266-149628273 chr6:149628264-149628273
13	FOS	chr6:149628090-149628419	MCF10A-Er-Src	breast:	n/a	chr6:149628262-149628270 chr6:149628266-149628273 chr6:149628264-149628273
14	NR3C1	chr6:149628086-149628536	A549	lung:	n/a	chr6:149628381-149628395 chr6:149628380-149628395
15	POLR2A	chr6:149628105-149628386	SK-N-SH	brain:	n/a	n/a
16	NR3C1	chr6:149628124-149628485	A549	lung:	n/a	chr6:149628381-149628395 chr6:149628380-149628395

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149625453..149629470-chr6:149636058..149640474,5	MCF-7	breast:

Variant related genes	Relation type
FABP12P1	TF binding region
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs491576	0.88[YRI][hapmap]
rs518836	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs533694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567049	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610237	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611454	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs632002	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1015360	chr6:149609804-149649982	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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 target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs661838	LRP11	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149627600-149628600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:149627800-149628600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:149627800-149628600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:149627800-149628800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:149627800-149629200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr6:149628000-149628600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:149628000-149628600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:149628000-149628800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr6:149628000-149628800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:149628000-149629400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:149628000-149629400	Enhancers	Osteobl	bone
12	chr6:149628000-149637800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:149628200-149628400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:149628200-149628400	Active TSS	A549	lung
15	chr6:149628200-149628600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:149628200-149628600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr6:149628200-149628600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:149628200-149628600	Enhancers	Brain Anterior Caudate	brain
19	chr6:149628200-149628600	Flanking Active TSS	HSMMtube	muscle
20	chr6:149628200-149628800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:149628200-149628800	Enhancers	NHDF-Ad	bronchial
22	chr6:149628200-149629200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:149628200-149629400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:149628200-149629400	Enhancers	NH-A	brain

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