Variant report

Variant	rs906351
Chromosome Location	chr1:209527925-209527926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:209424300..209425262-chr1:209527340..209528354,4	MCF-7	breast:
2	chr1:209524634..209532045-chr1:209599866..209610404,18	MCF-7	breast:
3	chr1:209421771..209422737-chr1:209527455..209528257,2	K562	blood:
4	chr1:209527807..209529591-chr1:209535703..209538583,2	MCF-7	breast:
5	chr1:209527253..209544360-chr1:209599669..209610889,45	MCF-7	breast:
6	chr1:209422633..209423473-chr1:209527733..209528276,2	MCF-7	breast:
7	chr1:209527510..209528253-chr1:209608740..209609589,5	MCF-7	breast:
8	chr1:209421788..209422593-chr1:209527401..209528229,3	MCF-7	breast:
9	chr1:209526627..209529456-chr1:209583930..209587370,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1014817	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1021993	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1027821	0.90[EUR][1000 genomes]
rs1027823	0.90[EUR][1000 genomes]
rs10494922	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10494924	0.83[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1354854	0.86[EUR][1000 genomes]
rs1395751	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1507341	0.87[EUR][1000 genomes]
rs17014326	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1857966	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2055698	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs2356722	0.80[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs2660636	0.88[EUR][1000 genomes]
rs2660640	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2660641	0.81[ASN][1000 genomes]
rs2660642	0.84[CEU][hapmap];0.80[CHB][hapmap];0.91[EUR][1000 genomes]
rs2660643	0.87[EUR][1000 genomes]
rs2843168	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6661759	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674103	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6674309	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685289	0.89[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6685498	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs906347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs906348	0.88[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs906349	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs906350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925077	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs937874	0.89[EUR][1000 genomes]
rs950890	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832492	chr1:209383771-209589312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs906351	LOC148696	cis	cerebellum	SCAN
rs906351	RAB7L1	cis	parietal	SCAN
rs906351	MDM4	cis	parietal	SCAN
rs906351	C1orf97	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209522800-209529200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:209523000-209529000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:209523200-209528000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:209523400-209529000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:209524800-209528000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:209525000-209528800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:209525200-209529800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:209526400-209528000	Enhancers	Fetal Brain Male	brain
9	chr1:209526400-209545600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:209527000-209529000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:209527000-209530800	Enhancers	HMEC	breast
12	chr1:209527200-209528400	Enhancers	Fetal Stomach	stomach
13	chr1:209527200-209528800	Enhancers	NHEK	skin
14	chr1:209527200-209531000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:209527400-209528000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:209527400-209528000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:209527400-209528000	Enhancers	Brain Anterior Caudate	brain
18	chr1:209527400-209528000	Enhancers	Fetal Muscle Leg	muscle
19	chr1:209527400-209528200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:209527400-209528200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:209527400-209528200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr1:209527400-209528200	Enhancers	Colon Smooth Muscle	Colon
23	chr1:209527400-209528200	Enhancers	Fetal Heart	heart
24	chr1:209527400-209528200	Enhancers	HSMM	muscle
25	chr1:209527400-209528400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:209527400-209529400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr1:209527400-209529400	Enhancers	Hela-S3	cervix
28	chr1:209527400-209530400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:209527400-209530800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:209527400-209530800	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr1:209527400-209530800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr1:209527600-209528200	Enhancers	Fetal Kidney	kidney
33	chr1:209527600-209530800	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr1:209527600-209530800	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr1:209527600-209530800	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr1:209527600-209531000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr1:209527800-209528200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:209527800-209528200	Weak transcription	Esophagus	oesophagus
39	chr1:209527800-209528400	Enhancers	Osteobl	bone
40	chr1:209527800-209529000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:209527800-209530200	Weak transcription	HSMMtube	muscle

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