Variant report

Variant	rs904506
Chromosome Location	chr1:224779653-224779654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224778814..224780539-chr1:224784357..224786736,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs56039603	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56403019	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58530774	0.92[ASN][1000 genomes]
rs6672413	0.92[CEU][hapmap];0.87[CHB][hapmap];0.92[EUR][1000 genomes]
rs6672806	0.93[CEU][hapmap];0.87[CHB][hapmap];0.88[EUR][1000 genomes]
rs6698799	0.93[CEU][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs880496	1.00[ASW][hapmap];0.89[CHB][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv873224	chr1:224746577-224794913	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3442947	chr1:224776590-224780847	Enhancers Genic enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs904506	CNIH3	cis	parietal	SCAN
rs904506	C1orf95	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224753600-224780400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:224767600-224779800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:224767800-224780200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:224768000-224780400	Weak transcription	Psoas Muscle	Psoas
5	chr1:224776800-224780400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:224777000-224780400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:224777200-224780200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:224777200-224780200	Weak transcription	HSMMtube	muscle
9	chr1:224777200-224780200	Weak transcription	NHDF-Ad	bronchial
10	chr1:224777200-224782200	Weak transcription	Aorta	Aorta
11	chr1:224777400-224780400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:224777400-224780400	Weak transcription	Osteobl	bone
13	chr1:224777400-224782000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:224777400-224782200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:224777400-224782200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:224777600-224780400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:224777600-224782200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:224779000-224781200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:224779200-224781200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:224779400-224780600	Enhancers	NH-A	brain
21	chr1:224779400-224781200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:224779600-224780600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:224779600-224781200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:224779600-224781600	Enhancers	HMEC	breast

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