Variant report

Variant	rs10745995
Chromosome Location	chr12:104657900-104657901
allele	C/T
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	EP300	chr12:104657152-104658189	SK-N-SH	brain:	n/a	n/a
2	FOS	chr12:104657474-104658164	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr12:104657645-104657912	MCF10A-Er-Src	breast:	n/a	n/a
4	GATA3	chr12:104657046-104658213	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr12:104656930-104658314	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr12:104657122-104658098	SK-N-SH	brain:	n/a	chr12:104657311-104657320
7	FOS	chr12:104657495-104658087	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr12:104657340-104658053	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:104657340-104658045	HL-60	blood:	n/a	n/a
10	POLR2A	chr12:104657590-104657957	MCF10A-Er-Src	breast:	n/a	n/a
11	SPI1	chr12:104657375-104657951	HL-60	blood:	n/a	n/a
12	JUND	chr12:104657147-104658162	SK-N-SH	brain:	n/a	n/a
13	NFIC	chr12:104657175-104658023	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr12:104657048-104658232	SK-N-SH	brain:	n/a	n/a
15	STAT3	chr12:104657589-104658018	MCF10A-Er-Src	breast:	n/a	n/a
16	PBX3	chr12:104657016-104658202	SK-N-SH	brain:	n/a	chr12:104657311-104657320
17	NFIC	chr12:104657139-104658213	SK-N-SH	brain:	n/a	n/a
18	TCF12	chr12:104656931-104658292	SK-N-SH	brain:	n/a	n/a
19	MYC	chr12:104657429-104658007	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr12:104657525-104658030	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr12:104657527-104658026	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104654376..104656180-chr12:104656602..104658713,2	K562	blood:

Variant related genes	Relation type
RPL18AP3	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10507174	1.00[MKK][hapmap]
rs10735392	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10735393	1.00[CEU][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.86[EUR][1000 genomes]
rs10735395	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10745996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs10778311	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs10778316	1.00[JPT][hapmap]
rs10778318	1.00[JPT][hapmap]
rs10778323	0.81[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs10861169	0.81[JPT][hapmap]
rs10861204	1.00[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11111943	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11111955	0.81[ASN][1000 genomes]
rs11111960	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs11111963	1.00[JPT][hapmap]
rs12424869	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17035324	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs17035504	0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs17192854	1.00[MKK][hapmap]
rs17202862	0.93[CEU][hapmap]
rs4129598	1.00[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs4246264	0.93[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4246269	1.00[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4246270	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4246271	1.00[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4388968	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4406890	0.81[JPT][hapmap]
rs4447242	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4502051	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4545635	1.00[ASW][hapmap];0.93[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4614534	1.00[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap]
rs4630362	1.00[CEU][hapmap]
rs4964227	0.93[CEU][hapmap]
rs4964228	0.93[CEU][hapmap]
rs4964257	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4964260	1.00[ASW][hapmap];0.93[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4964270	0.81[ASN][1000 genomes]
rs4964288	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4964627	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs4964735	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4964741	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964752	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964779	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4964784	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6419386	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6539137	1.00[CEU][hapmap]
rs6539138	0.81[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs7132418	0.86[CEU][hapmap]
rs7138035	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138317	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7138523	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs7139336	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294997	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298613	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7299866	1.00[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs7301631	0.91[JPT][hapmap]
rs7305872	0.81[AMR][1000 genomes]
rs73181916	0.83[AMR][1000 genomes]
rs7342395	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs7957725	0.86[CEU][hapmap]
rs7958851	0.83[ASN][1000 genomes]
rs7962423	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7969351	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7969380	0.87[ASN][1000 genomes]
rs7975161	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs7978101	0.81[AMR][1000 genomes]
rs9738614	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9739826	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9739833	1.00[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104652000-104669600	Weak transcription	Hela-S3	cervix
2	chr12:104652800-104673000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr12:104656200-104658200	Enhancers	A549	lung
4	chr12:104656200-104658400	Enhancers	HMEC	breast
5	chr12:104656400-104658200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:104656400-104658200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:104656600-104658200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:104656800-104658000	Enhancers	Stomach Mucosa	stomach
9	chr12:104656800-104658200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr12:104656800-104658200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:104656800-104658200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:104656800-104658200	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr12:104656800-104658600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:104657000-104658200	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr12:104657000-104658200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:104657000-104658200	Enhancers	HSMM	muscle
17	chr12:104657000-104658200	Enhancers	NHLF	lung
18	chr12:104657000-104658400	Enhancers	HSMMtube	muscle
19	chr12:104657000-104658800	Enhancers	NHDF-Ad	bronchial
20	chr12:104657200-104658200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr12:104657200-104658200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:104657200-104658200	Flanking Active TSS	NHEK	skin
23	chr12:104657200-104658400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr12:104657400-104658000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:104657400-104658000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr12:104657400-104658000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:104657400-104658000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:104657400-104658000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:104657400-104658200	Enhancers	H1 Cell Line	embryonic stem cell
30	chr12:104657400-104658200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr12:104657400-104658200	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr12:104657400-104658200	Enhancers	NH-A	brain
33	chr12:104657400-104658400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:104657400-104658400	Enhancers	Osteobl	bone
35	chr12:104657600-104658000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:104657600-104658000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr12:104657600-104658200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:104657600-104658200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:104657600-104658200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:104657600-104658200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:104657600-104658200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:104657800-104658200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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