Variant report

Variant	rs1465823
Chromosome Location	chr2:85976645-85976646
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr2:85976021-85976681	ECC-1	luminal epithelium:	n/a	n/a
2	TEAD4	chr2:85976112-85976758	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr2:85976580-85976730	AG04449	skin:	n/a	n/a
4	EP300	chr2:85975988-85976703	ECC-1	luminal epithelium:	n/a	n/a
5	SRF	chr2:85976092-85976747	ECC-1	luminal epithelium:	n/a	chr2:85976097-85976112 chr2:85976137-85976150 chr2:85976096-85976113
6	TEAD4	chr2:85976077-85976681	ECC-1	luminal epithelium:	n/a	n/a
7	CTCF	chr2:85976640-85976790	HFF	foreskin:	n/a	n/a
8	TCF12	chr2:85976083-85976681	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr2:85976218-85976815	ProgFib	skin:	n/a	n/a
10	CTCF	chr2:85976580-85976730	NHDF-neo	bronchial:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:85959891..85961430-chr2:85975278..85976868,2	MCF-7	breast:
2	chr2:85968047..85970017-chr2:85974638..85977440,3	MCF-7	breast:
3	chr2:85971643..85974209-chr2:85976098..85978084,3	MCF-7	breast:
4	chr2:85974895..85977251-chr2:85979669..85982640,2	MCF-7	breast:

Variant related genes	Relation type
ATOH8	TF binding region
ENSG00000168874	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10172667	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs1111527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1356621	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1356622	1.00[CEU][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1356623	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1356624	1.00[CEU][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1465822	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568310	0.93[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2118401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366816	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832007	0.93[CEU][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4832008	0.93[CEU][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4832190	0.93[CEU][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4832191	0.86[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs732155	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7557287	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567852	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv874468	chr2:85926598-86001255	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1012593	chr2:85966323-85997189	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv874469	chr2:85973618-86025251	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv874470	chr2:85973618-86028257	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv874471	chr2:85976645-86021919	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1465823	CAPG	cis	parietal	SCAN
rs1465823	CLIC2	trans	lymphoblastoid	seeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85971600-85977800	Weak transcription	Pancreas	Pancrea
2	chr2:85972400-85976800	Enhancers	Primary B cells from cord blood	blood
3	chr2:85972400-85978200	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:85972800-85977800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:85973000-85977800	Weak transcription	Brain Germinal Matrix	brain
6	chr2:85973000-85979000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:85973400-85980200	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr2:85973800-85977800	Weak transcription	Esophagus	oesophagus
9	chr2:85974600-85976800	Enhancers	Right Atrium	heart
10	chr2:85974600-85977600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr2:85974800-85980400	Enhancers	Fetal Heart	heart
12	chr2:85975000-85978000	Enhancers	Adipose Nuclei	Adipose
13	chr2:85975200-85976800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:85975200-85977000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr2:85975200-85977200	Enhancers	Psoas Muscle	Psoas
16	chr2:85975200-85977200	Enhancers	Right Ventricle	heart
17	chr2:85975200-85979400	Enhancers	Fetal Lung	lung
18	chr2:85975400-85977000	Bivalent Enhancer	Fetal Stomach	stomach
19	chr2:85975400-85977000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr2:85975400-85977200	Enhancers	Left Ventricle	heart
21	chr2:85975400-85977200	Enhancers	Lung	lung
22	chr2:85975600-85976800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:85975600-85976800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:85975600-85977200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr2:85975600-85979800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr2:85975600-85980000	Enhancers	Brain Substantia Nigra	brain
27	chr2:85975800-85976800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:85975800-85976800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr2:85975800-85977000	Enhancers	Aorta	Aorta
30	chr2:85975800-85977000	Enhancers	Rectal Smooth Muscle	rectum
31	chr2:85975800-85977200	Enhancers	NHDF-Ad	bronchial
32	chr2:85975800-85978800	Enhancers	Hela-S3	cervix
33	chr2:85975800-85979600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:85975800-85980000	Enhancers	HSMM	muscle
35	chr2:85975800-85980400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:85976000-85976800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:85976000-85976800	Enhancers	Ovary	ovary
38	chr2:85976000-85976800	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr2:85976000-85976800	Enhancers	NH-A	brain
40	chr2:85976000-85976800	Enhancers	NHLF	lung
41	chr2:85976000-85976800	Enhancers	Osteobl	bone
42	chr2:85976000-85977000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:85976000-85978600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr2:85976000-85978800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:85976000-85979600	Enhancers	Muscle Satellite Cultured Cells	--
46	chr2:85976000-85979800	Enhancers	Brain Hippocampus Middle	brain
47	chr2:85976000-85979800	Enhancers	A549	lung
48	chr2:85976200-85976800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:85976200-85976800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:85976200-85976800	Bivalent Enhancer	Placenta	Placenta

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