Variant report

Variant	rs3820231
Chromosome Location	chr1:225970284-225970285
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225963814..225970754-chr1:225996230..226002908,14	MCF-7	breast:
2	chr1:225966963..225971678-chr1:225973611..225976928,7	K562	blood:
3	chr1:225963461..225967975-chr1:225968057..225975345,14	MCF-7	breast:
4	chr1:225965161..225966858-chr1:225969808..225971572,2	MCF-7	breast:
5	chr1:225969775..225971862-chr1:226048864..226050541,2	K562	blood:
6	chr1:225969259..225971858-chr1:225998628..226000469,2	K562	blood:
7	chr1:225968570..225970564-chr1:226082071..226083838,2	K562	blood:
8	chr1:225955657..225958331-chr1:225968298..225970381,2	K562	blood:
9	chr1:225965000..225971731-chr1:226051573..226055609,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196187	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000143819	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1050033	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11583078	0.89[AFR][1000 genomes]
rs12031296	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12037640	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12042925	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045030	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12736440	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12737161	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12745281	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12749689	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1877724	1.00[JPT][hapmap]
rs2671274	0.86[AMR][1000 genomes]
rs56866192	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71646745	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71646746	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7539372	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3820231	C1orf115	cis	cerebellum	SCAN
rs3820231	TMEM63A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225966200-225973400	Weak transcription	Esophagus	oesophagus
2	chr1:225966800-225970400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:225966800-225972600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:225966800-225978600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:225967000-225970400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:225967000-225971800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr1:225967000-225972200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:225967000-225973600	Weak transcription	HSMMtube	muscle
9	chr1:225967200-225970600	Weak transcription	HSMM	muscle
10	chr1:225967200-225970800	Enhancers	Adipose Nuclei	Adipose
11	chr1:225967200-225971800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:225967200-225972200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:225967200-225972600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:225967200-225978400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:225967400-225971800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
16	chr1:225967400-225971800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:225967600-225970600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr1:225967600-225971000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:225967600-225971200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr1:225967600-225973600	Weak transcription	Fetal Kidney	kidney
21	chr1:225967800-225970600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr1:225967800-225970600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:225967800-225970800	Genic enhancers	K562	blood
24	chr1:225967800-225971200	Enhancers	Rectal Smooth Muscle	rectum
25	chr1:225967800-225971400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:225967800-225971600	Genic enhancers	Fetal Lung	lung
27	chr1:225967800-225971800	Enhancers	Brain Angular Gyrus	brain
28	chr1:225967800-225980200	Weak transcription	Stomach Mucosa	stomach
29	chr1:225968000-225970600	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:225968200-225970400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:225968200-225970600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
32	chr1:225968200-225970800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:225968200-225971000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:225968200-225971200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:225968200-225971200	Weak transcription	NH-A	brain
36	chr1:225968200-225971400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr1:225968200-225971600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:225968200-225972000	Weak transcription	Left Ventricle	heart
39	chr1:225968200-225972200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:225968200-225972200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:225968200-225972400	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:225968200-225972600	Weak transcription	Lung	lung
43	chr1:225968200-225972600	Weak transcription	Pancreas	Pancrea
44	chr1:225968200-225972800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:225968200-225972800	Weak transcription	Gastric	stomach
46	chr1:225968200-225972800	Weak transcription	Right Ventricle	heart
47	chr1:225968200-225973600	Weak transcription	Aorta	Aorta
48	chr1:225968200-225973600	Weak transcription	Colonic Mucosa	Colon
49	chr1:225968200-225980000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:225968400-225970400	Enhancers	Muscle Satellite Cultured Cells	--

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