Variant report

Variant	rs2120905
Chromosome Location	chr10:49773295-49773296
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	chr10:49761230..49763552-chr10:49773026..49775938,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1015921	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs10458722	0.93[ASN][1000 genomes]
rs10458723	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10458724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10458725	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10458726	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs10491040	0.83[CHD][hapmap]
rs10491041	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10491042	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10776618	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776619	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10776620	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10776621	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10857599	0.93[ASN][1000 genomes]
rs11101385	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs11101387	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1445166	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1579818	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[ASN][1000 genomes]
rs1814478	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1822863	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1838576	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1867589	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900023	0.88[ASN][1000 genomes]
rs2014513	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2120906	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2166225	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs2166227	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[ASN][1000 genomes]
rs3853764	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3853766	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3867454	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3867455	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3905490	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3925980	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3954086	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4101281	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4838426	0.88[ASN][1000 genomes]
rs4838626	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs4989810	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4989811	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61211884	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7068812	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7078307	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7085475	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7358030	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7358032	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7358134	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7358135	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs749377	0.81[GIH][hapmap];0.88[ASN][1000 genomes]
rs7907189	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7911176	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7919818	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs935295	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs935296	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs935297	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv6609	chr10:49770419-49778210	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2120905	RASSF4	cis	parietal	SCAN
rs2120905	ARHGAP22	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49742600-49774800	Weak transcription	Aorta	Aorta
2	chr10:49757400-49782200	Weak transcription	HSMMtube	muscle
3	chr10:49761600-49780600	Weak transcription	HUVEC	blood vessel
4	chr10:49763200-49780800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:49764400-49777800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr10:49765000-49773400	Weak transcription	NHLF	lung
7	chr10:49765000-49776400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:49765400-49774000	Weak transcription	NHDF-Ad	bronchial
9	chr10:49766000-49776800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:49770000-49775200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr10:49770600-49773400	Weak transcription	HSMM	muscle
12	chr10:49770800-49777400	Weak transcription	NH-A	brain
13	chr10:49771600-49779000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr10:49771800-49780200	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr10:49772000-49776800	Strong transcription	Osteobl	bone
16	chr10:49772400-49773600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr10:49772600-49773400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:49772600-49775200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:49772800-49773400	Enhancers	Brain Hippocampus Middle	brain
20	chr10:49773000-49782600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:49773000-49787400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr10:49773200-49774000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr10:49773200-49776200	Weak transcription	Brain Substantia Nigra	brain
24	chr10:49773200-49787800	Weak transcription	Brain Angular Gyrus	brain

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