Variant report

Variant	rs10922071
Chromosome Location	chr1:196433870-196433871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10494743	0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[ASN][1000 genomes]
rs10737670	0.87[CEU][hapmap]
rs10754187	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs10754188	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs10754196	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap]
rs10801530	0.86[CEU][hapmap]
rs10801531	0.82[CEU][hapmap]
rs10801532	0.86[GIH][hapmap];0.90[TSI][hapmap]
rs10801534	0.86[EUR][1000 genomes]
rs10801535	0.88[EUR][1000 genomes]
rs10801537	0.91[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10801538	0.86[CHB][hapmap];0.89[CHD][hapmap];0.93[ASN][1000 genomes]
rs10801539	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10801551	0.84[CHB][hapmap]
rs10922066	0.87[EUR][1000 genomes]
rs10922073	0.81[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs10922075	0.95[CHB][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10922078	0.89[EUR][1000 genomes]
rs10922082	0.82[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs10922083	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs10922084	0.82[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs10922088	0.80[CHB][hapmap]
rs11807331	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12065463	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12069983	0.87[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs12069990	0.87[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs12123128	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12562176	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs12729649	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs12738109	0.84[EUR][1000 genomes]
rs1416962	0.80[CHB][hapmap];0.81[CHD][hapmap];0.80[ASN][1000 genomes]
rs1538685	0.86[EUR][1000 genomes]
rs1538686	0.86[CHD][hapmap]
rs1538687	0.87[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs16840224	0.90[CHB][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap]
rs1769996	0.87[CEU][hapmap]
rs2027368	0.87[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs2878557	0.87[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2878558	0.86[EUR][1000 genomes]
rs3855964	0.87[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs3927686	0.87[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs3928857	0.87[CEU][hapmap];0.85[GIH][hapmap];0.84[EUR][1000 genomes]
rs4618911	0.81[CHB][hapmap]
rs4658039	0.81[CHB][hapmap]
rs60495441	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61820915	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678457	0.86[EUR][1000 genomes]
rs6680396	0.84[CHB][hapmap]
rs6696801	0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[ASN][1000 genomes]
rs6697795	0.89[EUR][1000 genomes]
rs72732257	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72732259	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7531611	0.87[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs7535696	0.87[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs7550015	0.86[EUR][1000 genomes]
rs869257	0.81[CHB][hapmap]
rs9427622	0.83[CHD][hapmap]
rs946750	0.87[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap]
rs946755	0.81[CHB][hapmap]

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	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1009233	chr1:196301712-196568874	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10922071	CFH	cis	parietal	SCAN
rs10922071	CLDN18	trans	parietal	SCAN
rs10922071	CFHR3	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196420000-196460800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:196425400-196434000	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:196429000-196435600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:196429200-196435400	Weak transcription	Ovary	ovary
5	chr1:196429200-196450400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:196430800-196439600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:196432000-196434600	Strong transcription	Liver	Liver
8	chr1:196432200-196437400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:196432800-196434200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:196433200-196436000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:196433200-196436400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:196433200-196437000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:196433400-196434400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:196433400-196434600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:196433400-196436000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:196433400-196436600	Enhancers	Osteobl	bone
17	chr1:196433600-196434400	Enhancers	Fetal Kidney	kidney
18	chr1:196433600-196434800	Enhancers	Colon Smooth Muscle	Colon
19	chr1:196433600-196435000	Enhancers	Rectal Smooth Muscle	rectum
20	chr1:196433600-196436600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:196433600-196436600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:196433600-196437800	Enhancers	NHDF-Ad	bronchial
23	chr1:196433600-196442200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:196433800-196434000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:196433800-196434200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:196433800-196434200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:196433800-196434200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:196433800-196434200	Enhancers	Fetal Stomach	stomach
29	chr1:196433800-196434400	Enhancers	NHLF	lung
30	chr1:196433800-196435000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:196433800-196436600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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