Variant report

Variant	rs958412
Chromosome Location	chr2:39187519-39187520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:82)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:82 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr2:39187412-39187792	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr2:39187498-39187685	GM19239	blood:	n/a	n/a
3	CTCF	chr2:39187478-39187657	Kidney_OC	kidney:	n/a	n/a
4	CTCF	chr2:39187460-39187610	HCFaa	heart:	n/a	n/a
5	NANOG	chr2:39187209-39187720	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr2:39186935-39188239	H1-hESC	embryonic stem cell:	n/a	n/a
7	TAF1	chr2:39187324-39187707	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr2:39187500-39187650	HPF	lung:	n/a	n/a
9	MAX	chr2:39187344-39187717	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr2:39187480-39187630	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr2:39187321-39187860	HUVEC	blood vessel:	n/a	n/a
12	CTCF	chr2:39187420-39187570	HBMEC	blood vessel:	n/a	n/a
13	USF2	chr2:39187203-39187615	H1-hESC	embryonic stem cell:	n/a	n/a
14	NRF1	chr2:39187297-39188144	SK-N-SH	brain:	n/a	chr2:39187955-39187964
15	TCF7L2	chr2:39187399-39187846	PANC-1	pancreas:	n/a	n/a
16	CTCF	chr2:39187268-39187654	H1-hESC	embryonic stem cell:	n/a	n/a
17	TBP	chr2:39187051-39187682	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr2:39187500-39187650	HEEpiC	esophagus:	n/a	n/a
19	CTCF	chr2:39187500-39187682	NHEK	skin:	n/a	n/a
20	CTCF	chr2:39187458-39187712	Fibrobl	skin:	n/a	n/a
21	CTCF	chr2:39187480-39187630	HMF	breast:	n/a	n/a
22	SP4	chr2:39187249-39187583	H1-hESC	embryonic stem cell:	n/a	n/a
23	SIN3A	chr2:39187482-39187726	H1-hESC	embryonic stem cell:	n/a	n/a
24	TEAD4	chr2:39187408-39187768	H1-hESC	embryonic stem cell:	n/a	n/a
25	MYC	chr2:39187473-39188006	H1-hESC	embryonic stem cell:	n/a	n/a
26	NRF1	chr2:39187453-39187865	GM12878	blood:	n/a	n/a
27	CTCF	chr2:39187480-39187630	AG04450	lung:	n/a	n/a
28	RAD21	chr2:39187415-39187764	IMR90	lung:	n/a	n/a
29	POLR2A	chr2:39187257-39187904	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr2:39187399-39187643	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr2:39187460-39187610	HA-sp	spinal cord:	n/a	n/a
32	POLR2A	chr2:39187115-39187751	HUVEC	blood vessel:	n/a	n/a
33	BACH1	chr2:39187406-39187896	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr2:39187340-39187610	SAEC	small airway:	n/a	n/a
35	CTCF	chr2:39187380-39187530	BJ	skin:	n/a	n/a
36	E2F6	chr2:39186598-39188433	H1-hESC	embryonic stem cell:	n/a	chr2:39186906-39186916 chr2:39187950-39187960 chr2:39187901-39187911
37	CTCF	chr2:39187497-39187635	SK-N-SH_RA	brain:	n/a	n/a
38	E2F6	chr2:39186760-39188342	H1-hESC	embryonic stem cell:	n/a	chr2:39186906-39186916 chr2:39187950-39187960 chr2:39187901-39187911
39	CTCF	chr2:39187500-39187650	GM12872	blood:	n/a	n/a
40	CTCF	chr2:39187380-39187530	HCM	heart:	n/a	n/a
41	CTCF	chr2:39187460-39187610	GM12866	blood:	n/a	n/a
42	CTCF	chr2:39187507-39187685	GM13977	blood:	n/a	n/a
43	CTCF	chr2:39187400-39187550	RPTEC	kidney:	n/a	n/a
44	NRF1	chr2:39187348-39188056	H1-hESC	embryonic stem cell:	n/a	chr2:39187955-39187964
45	CTCF	chr2:39187420-39187570	GM12869	blood:	n/a	n/a
46	TCF12	chr2:39187449-39187718	H1-hESC	embryonic stem cell:	n/a	n/a
47	RAD21	chr2:39187292-39187741	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr2:39187460-39187610	GM12875	blood:	n/a	n/a
49	CTCF	chr2:39187501-39187675	GM12891	blood:	n/a	n/a
50	CTCF	chr2:39187500-39187650	NHDF-neo	bronchial:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39183680..39185526-chr2:39186357..39188173,2	MCF-7	breast:

No data

Variant related genes	Relation type
ARHGEF33	TF binding region
ENSG00000269210	TF binding region
ENSG00000214694	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10172714	0.83[AMR][1000 genomes]
rs10186762	0.83[AMR][1000 genomes]
rs10201980	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13023273	0.83[AMR][1000 genomes]
rs1454221	0.83[AMR][1000 genomes]
rs1454222	0.83[AMR][1000 genomes]
rs1454223	0.83[AMR][1000 genomes]
rs1454225	0.83[AMR][1000 genomes]
rs1869513	0.83[EUR][1000 genomes]
rs1947432	0.83[AMR][1000 genomes]
rs2278912	0.83[AMR][1000 genomes]
rs2278913	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2278914	0.83[AMR][1000 genomes]
rs2290445	0.83[AMR][1000 genomes]
rs2305516	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs371745	0.81[EUR][1000 genomes]
rs4142729	0.83[AMR][1000 genomes]
rs4643520	0.83[AMR][1000 genomes]
rs4670269	0.81[EUR][1000 genomes]
rs4670270	0.83[AMR][1000 genomes]
rs4670901	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6544184	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6704656	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6716101	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6752850	0.83[AMR][1000 genomes]
rs6755527	0.83[AMR][1000 genomes]
rs7571052	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7573310	0.83[AMR][1000 genomes]
rs9679498	0.86[AMR][1000 genomes]

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	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs958412	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39186600-39187800	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr2:39186600-39188200	Enhancers	Fetal Brain Male	brain
3	chr2:39186600-39188400	Active TSS	Rectal Smooth Muscle	rectum
4	chr2:39186800-39187600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:39186800-39187600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr2:39186800-39188000	Active TSS	Brain Substantia Nigra	brain
7	chr2:39186800-39188000	Active TSS	Colon Smooth Muscle	Colon
8	chr2:39186800-39188000	Enhancers	Fetal Heart	heart
9	chr2:39186800-39188200	Active TSS	Brain Cingulate Gyrus	brain
10	chr2:39186800-39188200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr2:39186800-39188400	Active TSS	Brain Germinal Matrix	brain
12	chr2:39186800-39188400	Active TSS	Fetal Brain Female	brain
13	chr2:39187000-39187600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:39187000-39187600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:39187000-39187600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
16	chr2:39187000-39187600	Flanking Active TSS	Colonic Mucosa	Colon
17	chr2:39187000-39187600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
18	chr2:39187000-39187600	Flanking Active TSS	Gastric	stomach
19	chr2:39187000-39187600	Flanking Active TSS	Lung	lung
20	chr2:39187000-39187600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr2:39187000-39187600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
22	chr2:39187000-39187600	Flanking Active TSS	NH-A	brain
23	chr2:39187000-39187800	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr2:39187000-39187800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:39187000-39187800	Active TSS	Right Atrium	heart
26	chr2:39187000-39187800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr2:39187000-39188000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
28	chr2:39187000-39188000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:39187000-39188000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:39187000-39188000	Active TSS	Fetal Lung	lung
31	chr2:39187000-39188000	Flanking Bivalent TSS/Enh	Thymus	Thymus
32	chr2:39187000-39188000	Bivalent/Poised TSS	NHEK	skin
33	chr2:39187000-39188000	Active TSS	Osteobl	bone
34	chr2:39187000-39188200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:39187000-39188200	Active TSS	Brain Angular Gyrus	brain
36	chr2:39187000-39188200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:39187000-39188200	Active TSS	Fetal Kidney	kidney
38	chr2:39187000-39188200	Enhancers	Placenta	Placenta
39	chr2:39187000-39188200	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr2:39187000-39188200	Active TSS	NHLF	lung
41	chr2:39187200-39187600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:39187200-39187600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:39187200-39187600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr2:39187200-39187600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
45	chr2:39187200-39187600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:39187200-39187600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr2:39187200-39187600	Flanking Active TSS	Esophagus	oesophagus
48	chr2:39187200-39187600	Flanking Active TSS	Pancreas	Pancrea
49	chr2:39187200-39187600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr2:39187200-39187600	Active TSS	Rectal Mucosa Donor 31	rectum

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