Variant report

Variant	rs2073658
Chromosome Location	chr1:161010762-161010763
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160989087..160991942-chr1:161007144..161014242,6	K562	blood:
2	chr1:160988819..160994033-chr1:161005548..161011188,8	MCF-7	breast:
3	chr1:161007064..161010778-chr1:161101040..161104167,3	MCF-7	breast:
4	chr1:160988071..160992174-chr1:161007125..161014242,7	K562	blood:
5	chr1:161005808..161012985-chr1:161064732..161070101,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158769	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000158796	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1044478	0.87[AMR][1000 genomes]
rs1062826	0.89[AMR][1000 genomes]
rs1062827	0.89[AMR][1000 genomes]
rs11265540	0.83[AMR][1000 genomes]
rs11265542	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11799478	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11799521	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11801586	0.81[AMR][1000 genomes]
rs11807930	0.90[AMR][1000 genomes]
rs12401336	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12408778	0.82[AMR][1000 genomes]
rs12565932	0.89[AMR][1000 genomes]
rs17384360	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17388108	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1806774	0.86[AMR][1000 genomes]
rs2073655	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243427	0.84[AMR][1000 genomes]
rs2247459	0.84[AMR][1000 genomes]
rs2247596	0.82[AMR][1000 genomes]
rs2247671	0.84[AMR][1000 genomes]
rs2247790	0.84[AMR][1000 genomes]
rs2251597	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2251728	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2297219	0.89[AMR][1000 genomes]
rs2297220	0.89[AMR][1000 genomes]
rs2297221	0.89[AMR][1000 genomes]
rs2297222	0.89[AMR][1000 genomes]
rs2481080	0.84[AMR][1000 genomes]
rs2481081	0.84[AMR][1000 genomes]
rs2481083	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2481084	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2481085	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2483145	0.84[AMR][1000 genomes]
rs2774274	0.84[AMR][1000 genomes]
rs2988726	0.84[AMR][1000 genomes]
rs3119321	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3737785	0.89[AMR][1000 genomes]
rs3737787	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267947	0.89[AMR][1000 genomes]
rs41267949	0.89[AMR][1000 genomes]
rs41267951	0.89[AMR][1000 genomes]
rs41269993	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4339888	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55728374	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60315407	0.80[AMR][1000 genomes]
rs61803664	0.89[AMR][1000 genomes]
rs61803671	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61803672	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72712854	0.86[AMR][1000 genomes]
rs812741	0.84[AMR][1000 genomes]
rs836	0.88[AMR][1000 genomes]
rs869985	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv947201	chr1:161006051-161013276	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv548059	chr1:161007326-161010791	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv872492	chr1:161009523-161013152	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2073658	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161007000-161013400	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:161007400-161013400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:161007400-161013400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:161007400-161013400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:161007400-161013400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:161007600-161013400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:161008000-161013200	Strong transcription	A549	lung
8	chr1:161008000-161013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:161008200-161013000	Strong transcription	NHLF	lung
10	chr1:161008600-161011400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:161008800-161012600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:161008800-161013000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:161008800-161013400	Strong transcription	Brain Cingulate Gyrus	brain
14	chr1:161008800-161014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:161009000-161011800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:161009000-161012400	Weak transcription	Psoas Muscle	Psoas
17	chr1:161009000-161012600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:161009000-161012800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:161009000-161012800	Strong transcription	Adipose Nuclei	Adipose
20	chr1:161009000-161013200	Strong transcription	Osteobl	bone
21	chr1:161009000-161013400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:161009000-161013400	Strong transcription	Fetal Stomach	stomach
23	chr1:161009000-161014000	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr1:161009200-161012400	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr1:161009200-161012600	Strong transcription	Colon Smooth Muscle	Colon
26	chr1:161009200-161012800	Strong transcription	Aorta	Aorta
27	chr1:161009200-161012800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:161009200-161013000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:161009200-161013000	Strong transcription	Brain Substantia Nigra	brain
30	chr1:161009200-161013000	Strong transcription	HSMMtube	muscle
31	chr1:161009200-161013000	Strong transcription	HUVEC	blood vessel
32	chr1:161009200-161013200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:161009200-161013200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:161009200-161013200	Strong transcription	Fetal Kidney	kidney
35	chr1:161009200-161013200	Strong transcription	Hela-S3	cervix
36	chr1:161009200-161013200	Strong transcription	HepG2	liver
37	chr1:161009200-161013200	Strong transcription	NH-A	brain
38	chr1:161009200-161013200	Strong transcription	NHDF-Ad	bronchial
39	chr1:161009200-161013200	Strong transcription	NHEK	skin
40	chr1:161009200-161013400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:161009200-161013400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:161009200-161013400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:161009200-161013400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:161009200-161013400	Strong transcription	Brain Angular Gyrus	brain
45	chr1:161009200-161013400	Strong transcription	Brain Anterior Caudate	brain
46	chr1:161009200-161013400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:161009400-161011000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:161009400-161011200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:161009400-161011200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:161009400-161012000	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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