Variant report

Variant	rs587499
Chromosome Location	chr7:129077531-129077532
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:129075846..129077779-chr7:129107169..129109635,2	MCF-7	breast:
2	chr7:129075706..129078444-chr7:129101606..129103997,3	K562	blood:
3	chr7:129075012..129076890-chr7:129077253..129080120,2	MCF-7	breast:
4	chr7:129007735..129009248-chr7:129076789..129079028,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158467	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11768964	0.85[CHB][hapmap]
rs11771549	1.00[CHB][hapmap]
rs2598183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581829	0.85[CHB][hapmap]
rs586978	0.81[AFR][1000 genomes]
rs613068	0.85[CHB][hapmap];0.91[LWK][hapmap];0.86[YRI][hapmap]
rs639605	0.85[CHB][hapmap];0.86[YRI][hapmap]
rs655239	0.85[CHB][hapmap]
rs657664	0.85[CHB][hapmap]
rs676947	0.85[CHB][hapmap]
rs690872	0.85[CHB][hapmap];0.85[YRI][hapmap]
rs691183	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs691303	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs691325	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692132	0.85[CHB][hapmap]
rs692509	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692686	0.89[AFR][1000 genomes]
rs712692	0.88[AFR][1000 genomes]
rs712693	0.88[AFR][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	esv3331483	chr7:128918442-129082887	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1015550	chr7:128992460-129111060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv539122	chr7:128992460-129111060	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv831128	chr7:129063040-129240800	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs587499	FAM40B	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129075200-129078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:129075200-129083400	Weak transcription	Brain Substantia Nigra	brain
3	chr7:129075200-129088200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:129075200-129096000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr7:129075200-129100600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:129075200-129108400	Weak transcription	Gastric	stomach
7	chr7:129075400-129077600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:129075400-129078200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:129075400-129078400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:129075400-129078400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:129075400-129078400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:129075400-129078400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:129075400-129078400	Weak transcription	HSMMtube	muscle
14	chr7:129075400-129082800	Weak transcription	Fetal Muscle Leg	muscle
15	chr7:129075400-129085600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:129075400-129086000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr7:129075400-129093200	Weak transcription	Brain Angular Gyrus	brain
18	chr7:129075400-129102800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:129075400-129105800	Weak transcription	Ovary	ovary
20	chr7:129075600-129078000	Weak transcription	HUVEC	blood vessel
21	chr7:129075600-129078400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:129075600-129078400	Weak transcription	NH-A	brain
23	chr7:129075600-129078400	Enhancers	NHEK	skin
24	chr7:129075600-129078400	Weak transcription	NHLF	lung
25	chr7:129075600-129083400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:129075600-129083400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr7:129075600-129087600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr7:129075800-129078200	Weak transcription	Osteobl	bone
29	chr7:129075800-129078400	Weak transcription	NHDF-Ad	bronchial
30	chr7:129075800-129080000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:129075800-129080200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:129075800-129085400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr7:129075800-129087400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr7:129075800-129091800	Weak transcription	HepG2	liver
35	chr7:129076000-129079800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:129076000-129083600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr7:129076000-129088800	Weak transcription	Fetal Lung	lung
38	chr7:129076000-129095000	Weak transcription	Dnd41	blood
39	chr7:129076000-129110000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:129076400-129078400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr7:129076400-129085400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr7:129076400-129088000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr7:129076600-129077600	Enhancers	HMEC	breast
44	chr7:129076600-129078200	Weak transcription	Brain Anterior Caudate	brain
45	chr7:129076600-129078400	Enhancers	Muscle Satellite Cultured Cells	--
46	chr7:129076600-129078400	Weak transcription	Left Ventricle	heart
47	chr7:129076600-129078400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr7:129076600-129079800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr7:129076600-129083400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:129076600-129083400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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