Variant report

Variant	rs71541558
Chromosome Location	chr12:120662505-120662506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:120662009-120663961	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr12:120662183-120663758	U87	brain:	n/a	n/a
3	MAX	chr12:120662042-120662805	ECC-1	luminal epithelium:	n/a	chr12:120662565-120662574
4	MXI1	chr12:120662204-120662751	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:120661126-120671187	PANC-1	pancreas:	n/a	n/a
6	RAD21	chr12:120662244-120662534	Hela-S3	cervix:	n/a	chr12:120662423-120662435
7	ELF1	chr12:120662485-120663182	GM12878	blood:	n/a	n/a
8	NFYA	chr12:120662446-120662669	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr12:120661634-120662592	HUVEC	blood vessel:	n/a	n/a
10	ZNF143	chr12:120662366-120662553	Hela-S3	cervix:	n/a	n/a
11	CREB1	chr12:120662295-120662840	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr12:120662189-120662791	U87	brain:	n/a	n/a
13	POLR2A	chr12:120662067-120662826	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr12:120661800-120663088	Hela-S3	cervix:	n/a	n/a
15	TCF12	chr12:120662102-120663086	ECC-1	luminal epithelium:	n/a	chr12:120662594-120662602
16	ZNF263	chr12:120661264-120662633	HEK293-T-REx	kidney:	n/a	n/a
17	NFIC	chr12:120662169-120663207	ECC-1	luminal epithelium:	n/a	n/a
18	ZBTB7A	chr12:120662388-120663252	ECC-1	luminal epithelium:	n/a	n/a
19	RCOR1	chr12:120662178-120662716	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:120662107-120663290	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr12:120661913-120663084	ECC-1	luminal epithelium:	n/a	n/a
22	TCF7L2	chr12:120662266-120663112	Hela-S3	cervix:	n/a	n/a
23	NFIC	chr12:120662340-120663136	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr12:120662429-120662574	A549	lung:	n/a	n/a
25	POLR2A	chr12:120662348-120662618	A549	lung:	n/a	n/a
26	ELK1	chr12:120662333-120662527	Hela-S3	cervix:	n/a	n/a
27	MAZ	chr12:120662119-120663143	Hela-S3	cervix:	n/a	chr12:120662565-120662574
28	POLR2A	chr12:120662207-120662889	A549	lung:	n/a	n/a
29	POLR2A	chr12:120662060-120663238	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr12:120661985-120663196	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr12:120662168-120662934	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr12:120662314-120662936	GM18951	blood:	n/a	n/a
33	POLR2A	chr12:120662315-120662952	SK-N-MC	brain:	n/a	n/a
34	TAF1	chr12:120662302-120662644	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr12:120661780-120663894	K562	blood:	n/a	n/a
36	GTF2F1	chr12:120662249-120662758	Hela-S3	cervix:	n/a	n/a
37	MAX	chr12:120662123-120662624	Hela-S3	cervix:	n/a	chr12:120662565-120662574
38	CHD2	chr12:120662365-120662872	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr12:120661440-120664328	Hela-S3	cervix:	n/a	n/a
40	SMC3	chr12:120662169-120662723	Hela-S3	cervix:	n/a	chr12:120662328-120662335
41	BRCA1	chr12:120662211-120662614	Hela-S3	cervix:	n/a	n/a
42	MAX	chr12:120662195-120663233	ECC-1	luminal epithelium:	n/a	chr12:120662565-120662574
43	RFX5	chr12:120662175-120662690	Hela-S3	cervix:	n/a	n/a
44	TAF1	chr12:120662080-120662983	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120642171..120684465-chr12:120719749..120734210,267	K562	blood:
2	chr12:120628211..120641965-chr12:120660551..120674110,39	K562	blood:
3	chr12:120656223..120689871-chr12:120720394..120738112,311	MCF-7	breast:
4	chr12:120657004..120683911-chr12:120723753..120737731,232	K562	blood:

No data

Variant related genes	Relation type
PXN	TF binding region
ENSG00000089154	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000123009	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000200795	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1151821	0.93[ASN][1000 genomes]
rs1151822	0.89[ASN][1000 genomes]
rs1151823	0.96[ASN][1000 genomes]
rs1151826	0.96[ASN][1000 genomes]
rs1151828	0.96[ASN][1000 genomes]
rs1151833	0.96[ASN][1000 genomes]
rs1151835	0.96[ASN][1000 genomes]
rs1151836	0.96[ASN][1000 genomes]
rs1166788	0.96[ASN][1000 genomes]
rs1166789	0.91[ASN][1000 genomes]
rs1179386	0.91[ASN][1000 genomes]
rs12322327	0.91[ASN][1000 genomes]
rs12580333	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1632619	0.96[ASN][1000 genomes]
rs1634820	0.93[ASN][1000 genomes]
rs2239207	0.96[ASN][1000 genomes]
rs2283363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2701641	0.96[ASN][1000 genomes]
rs58777856	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs58919380	0.96[ASN][1000 genomes]
rs60134107	0.96[ASN][1000 genomes]
rs60282545	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61633133	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking 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 lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases
7	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
8	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120644000-120662600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:120647600-120662600	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:120647600-120662600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:120647600-120662600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:120647600-120662600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:120648000-120662800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr12:120648000-120662800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:120655200-120662600	Strong transcription	NHDF-Ad	bronchial
9	chr12:120655200-120665400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:120656200-120662600	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr12:120656200-120663200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:120656400-120664800	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:120656600-120663000	Strong transcription	NHLF	lung
14	chr12:120656800-120662800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:120656800-120666000	Weak transcription	Fetal Kidney	kidney
16	chr12:120657200-120662600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:120659400-120663000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:120660400-120662600	Weak transcription	Brain Germinal Matrix	brain
19	chr12:120660400-120666000	Weak transcription	Dnd41	blood
20	chr12:120660800-120662600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:120660800-120662600	Weak transcription	K562	blood
22	chr12:120660800-120663800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:120661200-120663000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:120661400-120662600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr12:120661400-120662600	Genic enhancers	NHEK	skin
26	chr12:120661400-120664600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:120661400-120664600	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr12:120661400-120664800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:120661400-120664800	Genic enhancers	HMEC	breast
30	chr12:120661600-120662600	Weak transcription	HSMMtube	muscle
31	chr12:120661600-120662800	Genic enhancers	Lung	lung
32	chr12:120661600-120664200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:120661600-120664200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:120661600-120664400	Genic enhancers	Osteobl	bone
35	chr12:120661600-120664600	Genic enhancers	Spleen	Spleen
36	chr12:120661600-120664800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
37	chr12:120661600-120666000	Genic enhancers	Muscle Satellite Cultured Cells	--
38	chr12:120661800-120662600	Weak transcription	Liver	Liver
39	chr12:120661800-120662600	Weak transcription	Fetal Brain Female	brain
40	chr12:120661800-120662600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
41	chr12:120661800-120662800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:120661800-120662800	Weak transcription	Brain Substantia Nigra	brain
43	chr12:120661800-120662800	Weak transcription	HSMM	muscle
44	chr12:120661800-120663000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:120661800-120663000	Active TSS	Stomach Mucosa	stomach
46	chr12:120661800-120663200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:120661800-120663200	Enhancers	Fetal Heart	heart
48	chr12:120661800-120663400	Weak transcription	Primary T cells from cord blood	blood
49	chr12:120661800-120663800	Flanking Active TSS	Hela-S3	cervix
50	chr12:120661800-120664000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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