Variant report

Variant	rs3820481
Chromosome Location	chr1:223942818-223942819
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:223941712-223945632	A549	lung:	n/a	n/a
2	POLR2A	chr1:223941795-223945620	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:223942529-223942825	K562	blood:	n/a	n/a
4	POLR2A	chr1:223942134-223945714	U87	brain:	n/a	n/a
5	POLR2A	chr1:223942371-223942867	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:223942464-223943974	K562	blood:	n/a	n/a
7	POLR2A	chr1:223942802-223943083	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr1:223937857-223950461	K562	blood:	n/a	n/a
9	POLR2A	chr1:223942006-223943197	U87	brain:	n/a	n/a
10	POLR2A	chr1:223942345-223944870	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223886105..223888614-chr1:223940802..223943504,3	K562	blood:
2	chr1:223901725..223903941-chr1:223941728..223943865,2	MCF-7	breast:
3	chr1:223940335..223944037-chr1:223947483..223951720,4	K562	blood:
4	chr1:223900402..223903093-chr1:223939885..223943104,3	K562	blood:
5	chr1:223941213..223943613-chr1:223960905..223963587,2	K562	blood:
6	chr1:223937037..223939857-chr1:223940065..223944617,5	K562	blood:
7	chr1:223886322..223888614-chr1:223940802..223943504,2	K562	blood:

No data

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10159015	0.83[ASN][1000 genomes]
rs12022914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12022920	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12022934	1.00[JPT][hapmap]
rs12024059	0.93[ASN][1000 genomes]
rs12025088	0.83[ASN][1000 genomes]
rs12026548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12027762	1.00[CHB][hapmap]
rs12028843	0.93[ASN][1000 genomes]
rs12031859	0.93[ASN][1000 genomes]
rs12034120	0.91[ASN][1000 genomes]
rs12034914	0.91[ASN][1000 genomes]
rs12035506	0.81[ASN][1000 genomes]
rs12036390	0.81[ASN][1000 genomes]
rs12036717	0.91[ASN][1000 genomes]
rs12037507	1.00[JPT][hapmap]
rs12038665	0.93[ASN][1000 genomes]
rs12038706	0.91[ASN][1000 genomes]
rs12039721	0.91[ASN][1000 genomes]
rs12040996	0.91[ASN][1000 genomes]
rs12043790	0.93[ASN][1000 genomes]
rs12044358	0.93[ASN][1000 genomes]
rs12044652	0.91[ASN][1000 genomes]
rs12044659	0.91[ASN][1000 genomes]
rs12047342	0.91[ASN][1000 genomes]
rs12048989	1.00[JPT][hapmap]
rs1542507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16842259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28370095	1.00[ASN][1000 genomes]
rs28370112	1.00[ASN][1000 genomes]
rs28370115	0.95[ASN][1000 genomes]
rs28370160	0.95[ASN][1000 genomes]
rs28370166	0.93[ASN][1000 genomes]
rs28370174	0.93[ASN][1000 genomes]
rs28370177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28370178	0.93[ASN][1000 genomes]
rs3754088	1.00[ASN][1000 genomes]
rs3767710	0.93[ASN][1000 genomes]
rs3767712	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs3767713	1.00[ASN][1000 genomes]
rs3820474	0.98[ASN][1000 genomes]
rs61437308	0.93[ASN][1000 genomes]
rs747811	0.93[ASN][1000 genomes]
rs7538151	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7552702	0.83[ASN][1000 genomes]
rs9804140	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9970756	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv520609	chr1:223931411-223947081	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv521758	chr1:223931411-223954080	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223931200-223954800	Strong transcription	HMEC	breast
2	chr1:223931400-223954400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:223935800-223952600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:223936600-223954800	Strong transcription	NHEK	skin
5	chr1:223936800-223947400	Weak transcription	Fetal Brain Male	brain
6	chr1:223936800-223954400	Strong transcription	HSMM	muscle
7	chr1:223937000-223943200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:223937000-223943400	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr1:223937000-223945400	Strong transcription	Hela-S3	cervix
10	chr1:223937000-223947600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:223937000-223948000	Strong transcription	Lung	lung
12	chr1:223937000-223948200	Weak transcription	Right Atrium	heart
13	chr1:223937000-223951200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:223937000-223954400	Strong transcription	Colonic Mucosa	Colon
15	chr1:223937000-223954400	Strong transcription	Esophagus	oesophagus
16	chr1:223937000-223954400	Strong transcription	Gastric	stomach
17	chr1:223937000-223954800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:223937000-223954800	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:223937000-223954800	Strong transcription	NHDF-Ad	bronchial
22	chr1:223937000-223954800	Strong transcription	Osteobl	bone
23	chr1:223937000-223957200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
26	chr1:223937200-223943000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:223937200-223948600	Strong transcription	HUVEC	blood vessel
28	chr1:223937200-223951800	Strong transcription	HSMMtube	muscle
29	chr1:223937200-223952600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:223937200-223953000	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:223937200-223954800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:223937200-223954800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:223937200-223954800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:223937200-223954800	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr1:223937200-223958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:223937200-223958400	Weak transcription	Fetal Heart	heart
37	chr1:223937400-223943200	Strong transcription	Brain Anterior Caudate	brain
38	chr1:223937400-223943200	Strong transcription	Brain Cingulate Gyrus	brain
39	chr1:223937400-223944200	Strong transcription	Fetal Lung	lung
40	chr1:223937400-223948600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:223937400-223948600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:223937400-223951000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:223937400-223952600	Strong transcription	NH-A	brain
44	chr1:223937400-223952800	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr1:223937400-223952800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:223937400-223953000	Strong transcription	Adipose Nuclei	Adipose
47	chr1:223937400-223954400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:223937400-223954400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:223937400-223954400	Strong transcription	NHLF	lung
50	chr1:223937400-223954800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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