Variant report

Variant	rs906348
Chromosome Location	chr1:209528346-209528347
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr1:209528146..209530754-chr1:209539138..209540797,2	MCF-7	breast:
4	chr1:209527807..209529591-chr1:209535703..209538583,2	MCF-7	breast:
5	chr1:209527253..209544360-chr1:209599669..209610889,45	MCF-7	breast:
6	chr1:209526627..209529456-chr1:209583930..209587370,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1014817	0.80[AFR][1000 genomes]
rs1021993	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1027821	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1027823	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10494922	0.82[AFR][1000 genomes]
rs10494924	0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1354854	0.88[EUR][1000 genomes]
rs1395751	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1507341	0.89[EUR][1000 genomes]
rs1857966	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2055698	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs2356722	0.85[CHB][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs2660636	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2660640	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2660642	0.84[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2660643	0.89[EUR][1000 genomes]
rs2843168	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661759	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6674103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674309	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6685289	0.88[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs906347	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs906349	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs906350	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs906351	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]
rs925077	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs937874	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs950890	0.83[AMR][1000 genomes];0.90[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
rs906348	RAB7L1	cis	parietal	SCAN
rs906348	C1orf97	cis	parietal	SCAN
rs906348	MDM4	cis	parietal	SCAN
rs906348	LOC148696	cis	cerebellum	SCAN

Chromatin state (count:32 , 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	chr1:209523400-209529000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:209525000-209528800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:209525200-209529800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:209526400-209545600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:209527000-209529000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:209527000-209530800	Enhancers	HMEC	breast
9	chr1:209527200-209528400	Enhancers	Fetal Stomach	stomach
10	chr1:209527200-209528800	Enhancers	NHEK	skin
11	chr1:209527200-209531000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:209527400-209528400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr1:209527400-209529400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr1:209527400-209529400	Enhancers	Hela-S3	cervix
15	chr1:209527400-209530400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:209527400-209530800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:209527400-209530800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr1:209527400-209530800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr1:209527600-209530800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr1:209527600-209530800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:209527600-209530800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr1:209527600-209531000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:209527800-209528400	Enhancers	Osteobl	bone
24	chr1:209527800-209529000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:209527800-209530200	Weak transcription	HSMMtube	muscle
26	chr1:209528000-209528400	Weak transcription	Fetal Brain Male	brain
27	chr1:209528000-209528800	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:209528000-209529600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:209528200-209528400	Enhancers	Esophagus	oesophagus
30	chr1:209528200-209529000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:209528200-209529600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:209528200-209530800	Enhancers	H9 Cell Line	embryonic stem cell

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