Variant report

Variant	rs55980956
Chromosome Location	chr12:121147222-121147223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:121147102-121147225	K562	blood:	n/a	n/a
2	POLR2A	chr12:121146918-121147371	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:121147121-121147244	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:121146570-121147249	HL-60	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:121147222-121147272	HepG2	liver:	n/a
2	chr12:121147222-121147272	HRPEpiC	eye:	n/a
3	chr12:121147222-121147272	GM12892	blood:	n/a
4	chr12:121147222-121147272	RPTEC	kidney:	n/a
5	chr12:121147222-121147272	SAEC	small airway:	n/a
6	chr12:121147222-121147272	PFSK-1	brain:	n/a
7	chr12:121147222-121147272	HUVEC	blood vessel:	n/a
8	chr12:121147222-121147272	GM06990	blood:	n/a
9	chr12:121147222-121147272	HRCEpiC	kidney:	n/a
10	chr12:121147222-121147272	NH-A	brain:	n/a
11	chr12:121147222-121147272	AG09309	skin:	n/a
12	chr12:121147222-121147272	MCF-7	breast:	n/a
13	chr12:121147222-121147272	AG10803	skin:	n/a
14	chr12:121147222-121147272	HCM	heart:	n/a
15	chr12:121147222-121147272	PrEC	prostate:	n/a
16	chr12:121147222-121147272	BE2_C	brain:	n/a
17	chr12:121147222-121147272	ProgFib	skin:	n/a
18	chr12:121147222-121147272	NB4	blood:	n/a
19	chr12:121147222-121147272	NHBE	bronchial:	n/a
20	chr12:121147222-121147272	MCF10A-Er-Src	breast:	n/a
21	chr12:121147222-121147272	AG09319	gingival:	n/a
22	chr12:121147222-121147272	SK-N-SH_RA	brain:	n/a
23	chr12:121147222-121147272	K562	blood:	n/a
24	chr12:121147222-121147272	HRE	kidney:	n/a
25	chr12:121147222-121147272	A549	lung:	n/a
26	chr12:121147222-121147272	LNCaP	prostate:	n/a
27	chr12:121147222-121147272	ECC-1	luminal epithelium:	n/a
28	chr12:121147222-121147272	HAEpiC	amniotic membrane:	n/a
29	chr12:121147222-121147272	HCF	heart:	n/a
30	chr12:121147222-121147272	GM12891	blood:	n/a
31	chr12:121147222-121147272	PANC-1	pancreas:	n/a
32	chr12:121147222-121147272	SKMC	muscle:	n/a
33	chr12:121147222-121147272	HIPEpiC	eye:	n/a
34	chr12:121147222-121147272	Caco-2	colon:	n/a
35	chr12:121147222-121147272	SK-N-MC	brain:	n/a
36	chr12:121147222-121147272	HL-60	blood:	n/a
37	chr12:121147222-121147272	Hela-S3	cervix:	n/a
38	chr12:121147222-121147272	AG04449	skin:	fetal
39	chr12:121147222-121147272	ovcar-3	ovarian:	n/a
40	chr12:121147222-121147272	HNPCEpiC	eye:	n/a
41	chr12:121147222-121147272	BJ	skin:	n/a
42	chr12:121147222-121147272	HMEC	breast:	n/a
43	chr12:121147222-121147272	HCT-116	colon:	n/a
44	chr12:121147222-121147272	NHDF-neo	bronchial:	n/a
45	chr12:121147222-121147272	NT2-D1	testis:	n/a
46	chr12:121147222-121147272	T-47D	breast:	n/a
47	chr12:121147222-121147272	HCPEpiC	choroid plexus:	n/a
48	chr12:121147222-121147272	AoSMC	blood vessel:	n/a
49	chr12:121147222-121147272	SK-N-SH	brain:	n/a
50	chr12:121147222-121147272	Hepatocyte	liver:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr12:121146305..121152610-chr12:121160959..121168394,8	MCF-7	breast:
2	chr12:121145921..121147941-chr12:121149529..121151514,2	MCF-7	breast:
3	chr12:121133471..121136112-chr12:121146959..121149468,2	MCF-7	breast:
4	chr12:121136411..121138197-chr12:121145701..121148306,2	K562	blood:
5	chr12:121122969..121126872-chr12:121145365..121151601,10	K562	blood:
6	chr12:121122617..121126013-chr12:121146742..121149972,4	MCF-7	breast:
7	chr12:121123292..121126341-chr12:121146632..121149740,5	MCF-7	breast:

No data

Variant related genes	Relation type
UNC119B	TF binding region
UNC119B	CpG island
ENSG00000265455	Chromatin interaction
ENSG00000110917	Chromatin interaction
ENSG00000256569	Chromatin interaction
ENSG00000256364	Chromatin interaction
ENSG00000122971	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs12821493	1.00[ASN][1000 genomes]
rs2138250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233673	1.00[ASN][1000 genomes]
rs35151295	1.00[ASN][1000 genomes]
rs35267083	1.00[ASN][1000 genomes]
rs3850521	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889470	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55645249	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55647329	1.00[ASN][1000 genomes]
rs55660947	1.00[ASN][1000 genomes]
rs55874815	1.00[ASN][1000 genomes]
rs55914930	1.00[ASN][1000 genomes]
rs55941696	1.00[ASN][1000 genomes]
rs55970240	1.00[ASN][1000 genomes]
rs56084677	1.00[ASN][1000 genomes]
rs56163702	1.00[ASN][1000 genomes]
rs56175661	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56178989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56183824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56189047	1.00[ASN][1000 genomes]
rs56206244	1.00[ASN][1000 genomes]
rs56231343	1.00[AFR][1000 genomes]
rs56284009	1.00[ASN][1000 genomes]
rs56366632	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56391085	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56401401	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58235352	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73213106	1.00[ASN][1000 genomes]
rs73214885	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73214888	1.00[ASN][1000 genomes]
rs73214894	1.00[ASN][1000 genomes]
rs73214896	1.00[ASN][1000 genomes]
rs73217009	1.00[ASN][1000 genomes]
rs73217017	1.00[ASN][1000 genomes]
rs73222694	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73222699	1.00[ASN][1000 genomes]
rs73222778	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73222780	1.00[ASN][1000 genomes]
rs73222784	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73222786	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73222787	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs73222794	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73222795	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73224303	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73224309	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73224313	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73225003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73225012	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73225023	1.00[ASN][1000 genomes]
rs73225093	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73225101	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73227016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73227022	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73227026	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73227027	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73227029	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73227033	1.00[ASN][1000 genomes]
rs73227036	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73227038	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73229118	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73229126	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73229149	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73229151	1.00[ASN][1000 genomes]
rs73229157	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73229160	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73229162	1.00[ASN][1000 genomes]
rs73230347	1.00[ASN][1000 genomes]
rs73230349	1.00[ASN][1000 genomes]
rs73230352	1.00[AFR][1000 genomes];1.00[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121127600-121147600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:121135400-121147400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:121135600-121147400	Weak transcription	Fetal Brain Male	brain
4	chr12:121136000-121147600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:121136200-121147400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:121136400-121147400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:121136400-121147600	Weak transcription	Stomach Mucosa	stomach
8	chr12:121136600-121147800	Weak transcription	NHDF-Ad	bronchial
9	chr12:121138200-121147600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:121138200-121147600	Weak transcription	Hela-S3	cervix
11	chr12:121138400-121147600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:121138400-121147600	Weak transcription	NH-A	brain
13	chr12:121138800-121147800	Weak transcription	Small Intestine	intestine
14	chr12:121139000-121147400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:121139200-121147400	Weak transcription	Fetal Kidney	kidney
16	chr12:121139400-121147800	Weak transcription	Esophagus	oesophagus
17	chr12:121139400-121147800	Weak transcription	Psoas Muscle	Psoas
18	chr12:121139600-121147400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:121139800-121147600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:121140000-121147400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:121140000-121147400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:121140000-121147400	Weak transcription	Brain Substantia Nigra	brain
23	chr12:121140000-121147600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:121140200-121147400	Weak transcription	Brain Anterior Caudate	brain
25	chr12:121140200-121147400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:121140200-121147400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:121140200-121147400	Weak transcription	K562	blood
28	chr12:121140200-121147600	Weak transcription	HMEC	breast
29	chr12:121140200-121147800	Weak transcription	HUVEC	blood vessel
30	chr12:121140400-121147600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:121140400-121147600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr12:121140600-121147400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:121140600-121147400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:121140600-121147600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:121140600-121147600	Weak transcription	Primary B cells from cord blood	blood
36	chr12:121140800-121147400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:121140800-121147400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr12:121140800-121147400	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:121140800-121147400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:121140800-121147600	Weak transcription	Colonic Mucosa	Colon
41	chr12:121140800-121147800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:121141000-121147400	Weak transcription	Pancreas	Pancrea
43	chr12:121141000-121147600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:121141000-121147600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr12:121141200-121147400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr12:121141200-121147400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr12:121141200-121147400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr12:121141200-121147600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:121141200-121147600	Weak transcription	Spleen	Spleen
50	chr12:121141200-121147600	Weak transcription	NHLF	lung

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