Variant report

Variant	rs2306893
Chromosome Location	chr12:10251650-10251651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:10251465-10251724	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:10251322-10251752	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr12:10251392-10251671	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr12:10251383-10251786	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZNF143	chr12:10251433-10251714	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr12:10251422-10251816	H1-hESC	embryonic stem cell:	n/a	n/a
7	TAF1	chr12:10251401-10251736	H1-hESC	embryonic stem cell:	n/a	n/a
8	TEAD4	chr12:10251371-10251795	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:10251338-10251799	HUVEC	blood vessel:	n/a	n/a
10	TBP	chr12:10251472-10251652	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr12:10251256-10251829	HUVEC	blood vessel:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:10251638-10251688	HIPEpiC	eye:	n/a
2	chr12:10251638-10251688	HCF	heart:	n/a
3	chr12:10251638-10251688	Caco-2	colon:	n/a
4	chr12:10251638-10251688	U87	brain:	n/a
5	chr12:10251638-10251688	SAEC	small airway:	n/a
6	chr12:10251638-10251688	PFSK-1	brain:	n/a
7	chr12:10251638-10251688	AG09309	skin:	n/a
8	chr12:10251638-10251688	GM12892	blood:	n/a
9	chr12:10251638-10251688	A549	lung:	n/a
10	chr12:10251638-10251688	CMK	blood:	n/a
11	chr12:10251638-10251688	HEEpiC	esophagus:	n/a
12	chr12:10251638-10251688	HAEpiC	amniotic membrane:	n/a
13	chr12:10251638-10251688	ECC-1	luminal epithelium:	n/a
14	chr12:10251638-10251688	NH-A	brain:	n/a
15	chr12:10251638-10251688	SK-N-SH	brain:	n/a
16	chr12:10251638-10251688	LNCaP	prostate:	n/a
17	chr12:10251638-10251688	GM12878	blood:	n/a
18	chr12:10251638-10251688	AG10803	skin:	n/a
19	chr12:10251638-10251688	GM12891	blood:	n/a
20	chr12:10251638-10251688	Jurkat	blood:	n/a
21	chr12:10251638-10251688	AG04449	skin:	fetal
22	chr12:10251638-10251688	HUVEC	blood vessel:	n/a
23	chr12:10251638-10251688	NB4	blood:	n/a
24	chr12:10251638-10251688	T-47D	breast:	n/a
25	chr12:10251638-10251688	IMR90	lung:	fetal
26	chr12:10251638-10251688	Hepatocyte	liver:	n/a
27	chr12:10251638-10251688	NT2-D1	testis:	n/a
28	chr12:10251638-10251688	AoSMC	blood vessel:	n/a
29	chr12:10251638-10251688	HRE	kidney:	n/a
30	chr12:10251638-10251688	HRCEpiC	kidney:	n/a
31	chr12:10251638-10251688	HMEC	breast:	n/a
32	chr12:10251638-10251688	ProgFib	skin:	n/a
33	chr12:10251638-10251688	H1-hESC	embryonic stem cell:	embryo
34	chr12:10251638-10251688	MCF-7	breast:	n/a
35	chr12:10251638-10251688	AG04450	lung:	fetal
36	chr12:10251638-10251688	ovcar-3	ovarian:	n/a
37	chr12:10251638-10251688	PrEC	prostate:	n/a
38	chr12:10251638-10251688	SKMC	muscle:	n/a
39	chr12:10251638-10251688	HNPCEpiC	eye:	n/a
40	chr12:10251638-10251688	HepG2	liver:	n/a
41	chr12:10251638-10251688	HCPEpiC	choroid plexus:	n/a
42	chr12:10251638-10251688	HCT-116	colon:	n/a
43	chr12:10251638-10251688	SK-N-MC	brain:	n/a
44	chr12:10251638-10251688	PANC-1	pancreas:	n/a
45	chr12:10251638-10251688	HCM	heart:	n/a
46	chr12:10251638-10251688	Hela-S3	cervix:	n/a
47	chr12:10251638-10251688	HL-60	blood:	n/a
48	chr12:10251638-10251688	BJ	skin:	n/a
49	chr12:10251638-10251688	HEK293	kidney:	embryo
50	chr12:10251638-10251688	MCF10A-Er-Src	breast:	n/a

No data

Variant related genes	Relation type
CLEC1A	TF binding region
CLEC1A	CpG island

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10772231	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772234	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845032	0.90[EUR][1000 genomes]
rs10845035	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845037	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845038	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845039	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845040	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11053577	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11053578	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053579	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053580	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11053589	0.90[CHB][hapmap]
rs12300167	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12370211	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12372259	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12372577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1352477	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1387140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1948184	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1948185	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2087304	0.92[ASN][1000 genomes]
rs2087305	0.92[ASN][1000 genomes]
rs2087306	0.89[ASN][1000 genomes]
rs2087307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2220436	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277416	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2306891	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306892	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306894	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2401600	0.98[ASN][1000 genomes]
rs2401601	0.98[ASN][1000 genomes]
rs2401602	0.96[ASN][1000 genomes]
rs2401603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2401604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2401605	0.98[ASN][1000 genomes]
rs2401606	0.98[ASN][1000 genomes]
rs2401607	0.98[ASN][1000 genomes]
rs2401611	0.81[ASN][1000 genomes]
rs2401614	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2401615	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2401616	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816845	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825300	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3886137	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3886143	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3887490	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3912644	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3912645	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3994131	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3994132	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4265666	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4499082	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4595634	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4764247	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4764248	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4764249	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4764250	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4764251	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5012088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6416262	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6416263	0.98[ASN][1000 genomes]
rs6488249	1.00[CEU][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6488250	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6488252	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6488253	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6488254	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6488256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6488257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6488258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488259	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488261	0.88[ASN][1000 genomes]
rs7313750	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7953886	1.00[CEU][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7956208	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956327	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7957278	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7960611	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7962246	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7962341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969125	1.00[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7970083	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972187	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7974909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7976945	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7977902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7979762	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7980801	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs952545	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs952546	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10242800-10253800	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:10245800-10251800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:10247800-10252400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:10249000-10252000	Active TSS	Right Atrium	heart
5	chr12:10249600-10253400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:10250200-10253800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:10250600-10252400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr12:10250600-10254200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:10251000-10251800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr12:10251000-10252000	Enhancers	Fetal Stomach	stomach
11	chr12:10251000-10254600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr12:10251200-10251800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr12:10251200-10251800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:10251200-10252000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr12:10251200-10252000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr12:10251200-10252000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr12:10251200-10252000	Enhancers	Fetal Intestine Small	intestine
18	chr12:10251200-10252200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:10251200-10252400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr12:10251200-10252600	Enhancers	Placenta Amnion	Placenta Amnion
21	chr12:10251400-10251800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:10251400-10251800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:10251400-10251800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:10251400-10251800	Enhancers	Esophagus	oesophagus
25	chr12:10251400-10251800	Enhancers	Fetal Muscle Trunk	muscle
26	chr12:10251400-10252000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:10251400-10255400	Enhancers	Placenta	Placenta
28	chr12:10251600-10251800	Enhancers	Stomach Smooth Muscle	stomach
29	chr12:10251600-10252000	Enhancers	HUVEC	blood vessel
30	chr12:10251600-10252200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr12:10251600-10252400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:10251600-10253400	Weak transcription	Adipose Nuclei	Adipose
33	chr12:10251600-10253400	Weak transcription	Fetal Kidney	kidney
34	chr12:10251600-10253400	Weak transcription	Fetal Lung	lung
35	chr12:10251600-10253400	Weak transcription	Fetal Muscle Leg	muscle
36	chr12:10251600-10253400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:10251600-10253600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:10251600-10253600	Weak transcription	Left Ventricle	heart
39	chr12:10251600-10253600	Weak transcription	Lung	lung
40	chr12:10251600-10253800	Weak transcription	Fetal Thymus	thymus
41	chr12:10251600-10253800	Weak transcription	Ovary	ovary

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