Variant report

Variant	rs2118401
Chromosome Location	chr2:85977273-85977274
allele	C/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	RAD21	chr2:85977185-85978407	SK-N-SH	brain:	n/a	chr2:85977801-85977820
2	CTCF	chr2:85977248-85978410	A549	lung:	n/a	chr2:85977803-85977812 chr2:85977803-85977816 chr2:85977801-85977817 chr2:85977805-85977815 chr2:85977802-85977823 chr2:85977800-85977818

No.	Distal block	Cell Line	Cell type
1	chr2:85976745..85979342-chr2:85979775..85983018,3	K562	blood:
2	chr2:85976940..85977835-chr2:85988194..85989005,2	K562	blood:
3	chr2:85968047..85970017-chr2:85974638..85977440,3	MCF-7	breast:
4	chr2:85971643..85974209-chr2:85976098..85978084,3	MCF-7	breast:
5	chr2:85976672..85979342-chr2:85979775..85983871,4	K562	blood:

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];0.83[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];0.98[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];0.93[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];0.92[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];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[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];0.90[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];0.97[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]
rs1465823	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]
rs1473275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1568310	0.93[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2366816	1.00[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];0.89[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];0.89[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];0.94[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
rs2118401	CAPG	cis	parietal	SCAN
rs2118401	CLIC2	trans	lymphoblastoid	seeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85971600-85977800	Weak transcription	Pancreas	Pancrea
2	chr2:85972400-85978200	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:85972800-85977800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:85973000-85977800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:85973000-85979000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:85973400-85980200	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr2:85973800-85977800	Weak transcription	Esophagus	oesophagus
8	chr2:85974600-85977600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr2:85974800-85980400	Enhancers	Fetal Heart	heart
10	chr2:85975000-85978000	Enhancers	Adipose Nuclei	Adipose
11	chr2:85975200-85979400	Enhancers	Fetal Lung	lung
12	chr2:85975600-85979800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:85975600-85980000	Enhancers	Brain Substantia Nigra	brain
14	chr2:85975800-85978800	Enhancers	Hela-S3	cervix
15	chr2:85975800-85979600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:85975800-85980000	Enhancers	HSMM	muscle
17	chr2:85975800-85980400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:85976000-85978600	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr2:85976000-85978800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:85976000-85979600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:85976000-85979800	Enhancers	Brain Hippocampus Middle	brain
22	chr2:85976000-85979800	Enhancers	A549	lung
23	chr2:85976200-85977600	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr2:85976600-85977600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr2:85976600-85977800	Weak transcription	Liver	Liver
26	chr2:85976600-85977800	Weak transcription	Brain Angular Gyrus	brain
27	chr2:85976600-85977800	Weak transcription	Spleen	Spleen
28	chr2:85976600-85979000	Enhancers	HSMMtube	muscle
29	chr2:85976600-85980200	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr2:85976800-85977600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:85976800-85977600	Weak transcription	Osteobl	bone
32	chr2:85976800-85977800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:85976800-85977800	Weak transcription	Primary B cells from cord blood	blood
34	chr2:85976800-85977800	Weak transcription	Ovary	ovary
35	chr2:85976800-85977800	Weak transcription	Right Atrium	heart
36	chr2:85976800-85977800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:85976800-85977800	Weak transcription	Stomach Mucosa	stomach
38	chr2:85976800-85977800	Weak transcription	NHLF	lung
39	chr2:85976800-85978000	Weak transcription	Brain Anterior Caudate	brain
40	chr2:85976800-85978200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:85976800-85978200	Enhancers	Stomach Smooth Muscle	stomach
42	chr2:85976800-85979000	Enhancers	Colon Smooth Muscle	Colon
43	chr2:85977000-85977400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:85977000-85977600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:85977000-85980000	Weak transcription	Gastric	stomach
46	chr2:85977000-85980200	Weak transcription	Aorta	Aorta
47	chr2:85977200-85977600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:85977200-85977600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:85977200-85977600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:85977200-85977600	Weak transcription	Left Ventricle	heart

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