Variant report

Variant	rs1153958
Chromosome Location	chr1:223943817-223943818
allele	C/G
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	POLR2A	chr1:223941712-223945632	A549	lung:	n/a	n/a
2	POLR2A	chr1:223941795-223945620	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr1:223943809-223943978	MCF-7	breast:	n/a	n/a
4	POLR2A	chr1:223943494-223945154	K562	blood:	n/a	n/a
5	CTCF	chr1:223943800-223943950	HCPEpiC	choroid plexus:	n/a	n/a
6	POLR2A	chr1:223942134-223945714	U87	brain:	n/a	n/a
7	RAD21	chr1:223943735-223944036	H1-hESC	embryonic stem cell:	n/a	chr1:223943897-223943909 chr1:223943811-223943821 chr1:223943897-223943907
8	CTCF	chr1:223943808-223944001	MCF-7	breast:	n/a	n/a
9	RAD21	chr1:223943659-223944204	MCF-7	breast:	n/a	chr1:223943897-223943909 chr1:223943811-223943821 chr1:223943897-223943907
10	RAD21	chr1:223943756-223944058	HepG2	liver:	n/a	chr1:223943897-223943909 chr1:223943811-223943821 chr1:223943897-223943907
11	RAD21	chr1:223943716-223944169	MCF-7	breast:	n/a	chr1:223943897-223943909 chr1:223943811-223943821 chr1:223943897-223943907
12	CTCF	chr1:223943795-223944004	MCF-7	breast:	n/a	n/a
13	POLR2A	chr1:223943345-223944175	K562	blood:	n/a	n/a
14	POLR2A	chr1:223943238-223945714	U87	brain:	n/a	n/a
15	CTCF	chr1:223943778-223944097	MCF-7	breast:	n/a	n/a
16	POLR2A	chr1:223943577-223944840	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:223942464-223943974	K562	blood:	n/a	n/a
18	CTCF	chr1:223943800-223943950	HPAF	blood vessel:	n/a	n/a
19	CTCF	chr1:223943719-223944112	MCF-7	breast:	n/a	n/a
20	CTCF	chr1:223943790-223944007	MCF-7	breast:	n/a	n/a
21	CTCF	chr1:223943786-223944007	MCF-7	breast:	n/a	n/a
22	POLR2A	chr1:223937857-223950461	K562	blood:	n/a	n/a
23	CTCF	chr1:223943800-223943950	HRPEpiC	eye:	n/a	n/a
24	POLR2A	chr1:223943487-223944859	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr1:223943446-223944237	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr1:223943641-223943931	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:223943506-223943864	K562	blood:	n/a	n/a
28	POLR2A	chr1:223942345-223944870	K562	blood:	n/a	n/a
29	POLR2A	chr1:223943689-223943834	HUVEC	blood vessel:	n/a	n/a
30	CTCF	chr1:223943760-223943910	HRPEpiC	eye:	n/a	n/a
31	CTCF	chr1:223943760-223943910	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:223901725..223903941-chr1:223941728..223943865,2	MCF-7	breast:
2	chr1:223940335..223944037-chr1:223947483..223951720,4	K562	blood:
3	chr1:223937037..223939857-chr1:223940065..223944617,5	K562	blood:
4	chr1:223891679..223894044-chr1:223943117..223944759,2	MCF-7	breast:

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

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10159015	0.97[EUR][1000 genomes]
rs10465524	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1153957	0.96[EUR][1000 genomes]
rs1153965	0.81[EUR][1000 genomes]
rs12059128	0.82[EUR][1000 genomes]
rs12059770	0.82[EUR][1000 genomes]
rs12060361	0.82[EUR][1000 genomes]
rs12080250	0.85[EUR][1000 genomes]
rs12088254	0.81[EUR][1000 genomes]
rs12091841	0.82[EUR][1000 genomes]
rs1222077	0.95[EUR][1000 genomes]
rs12563291	0.87[ASN][1000 genomes]
rs12563477	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12563637	0.87[ASN][1000 genomes]
rs12563695	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12563713	0.87[ASN][1000 genomes]
rs12565967	0.82[EUR][1000 genomes]
rs16842162	0.85[EUR][1000 genomes]
rs16842229	0.82[EUR][1000 genomes]
rs17597	0.87[ASN][1000 genomes]
rs28370043	0.87[ASN][1000 genomes]
rs28370073	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28370074	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28370088	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28370159	0.81[EUR][1000 genomes]
rs28370170	0.85[EUR][1000 genomes]
rs34683843	0.82[EUR][1000 genomes]
rs3885657	0.82[EUR][1000 genomes]
rs61824003	0.85[EUR][1000 genomes]
rs61824005	0.81[EUR][1000 genomes]
rs61824008	0.82[EUR][1000 genomes]
rs6604724	0.82[EUR][1000 genomes]
rs6682964	0.82[EUR][1000 genomes]
rs6685557	0.82[EUR][1000 genomes]
rs6691315	0.82[EUR][1000 genomes]
rs6694960	0.82[EUR][1000 genomes]
rs6696053	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7331	0.85[EUR][1000 genomes]
rs7530328	0.82[EUR][1000 genomes]
rs7533551	0.82[EUR][1000 genomes]
rs7548911	0.86[EUR][1000 genomes]
rs7552702	0.97[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1153958	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

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	chr1:223937000-223945400	Strong transcription	Hela-S3	cervix
8	chr1:223937000-223947600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:223937000-223948000	Strong transcription	Lung	lung
10	chr1:223937000-223948200	Weak transcription	Right Atrium	heart
11	chr1:223937000-223951200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:223937000-223954400	Strong transcription	Colonic Mucosa	Colon
13	chr1:223937000-223954400	Strong transcription	Esophagus	oesophagus
14	chr1:223937000-223954400	Strong transcription	Gastric	stomach
15	chr1:223937000-223954800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:223937000-223954800	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:223937000-223954800	Strong transcription	NHDF-Ad	bronchial
20	chr1:223937000-223954800	Strong transcription	Osteobl	bone
21	chr1:223937000-223957200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
24	chr1:223937200-223948600	Strong transcription	HUVEC	blood vessel
25	chr1:223937200-223951800	Strong transcription	HSMMtube	muscle
26	chr1:223937200-223952600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:223937200-223953000	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:223937200-223954800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:223937200-223954800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:223937200-223954800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:223937200-223954800	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr1:223937200-223958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:223937200-223958400	Weak transcription	Fetal Heart	heart
34	chr1:223937400-223944200	Strong transcription	Fetal Lung	lung
35	chr1:223937400-223948600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:223937400-223948600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:223937400-223951000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:223937400-223952600	Strong transcription	NH-A	brain
39	chr1:223937400-223952800	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr1:223937400-223952800	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:223937400-223953000	Strong transcription	Adipose Nuclei	Adipose
42	chr1:223937400-223954400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr1:223937400-223954400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:223937400-223954400	Strong transcription	NHLF	lung
45	chr1:223937400-223954800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:223937400-223954800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:223937400-223954800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:223937400-223954800	Strong transcription	Fetal Stomach	stomach
49	chr1:223937400-223954800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:223937400-223954800	Strong transcription	A549	lung

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