Variant report

Variant	rs1909203
Chromosome Location	chr1:77952669-77952670
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	chr1:77948475..77951287-chr1:77952444..77954143,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12733666	1.00[CHD][hapmap];0.83[MEX][hapmap]
rs12751064	1.00[CHD][hapmap]
rs17381664	1.00[CHD][hapmap]
rs1909202	1.00[CHD][hapmap]
rs2454328	0.81[AFR][1000 genomes]
rs2647497	0.91[ASW][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4949662	1.00[CHD][hapmap]
rs4949803	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[ASN][1000 genomes]
rs6678622	1.00[CHD][hapmap]
rs6684022	1.00[CHD][hapmap]

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	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1909203	MSH4	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77913200-77968400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr1:77914600-77955600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:77934600-77955200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:77935600-77955800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:77935800-77954800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:77940200-77955800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:77940400-77954800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:77940400-77955400	Weak transcription	NHLF	lung
9	chr1:77940600-77954800	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:77940600-77955600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:77940600-77960800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:77940800-77955400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:77944800-77955400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:77945400-77958600	Weak transcription	Primary T cells from cord blood	blood
15	chr1:77945800-77961600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:77947000-77953400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:77947000-77954400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:77947000-77954800	Weak transcription	Brain Substantia Nigra	brain
19	chr1:77951800-77953400	Strong transcription	NHDF-Ad	bronchial
20	chr1:77951800-77953600	Strong transcription	HSMM	muscle
21	chr1:77952000-77954200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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