Variant report

Variant	rs12133722
Chromosome Location	chr1:85873237-85873238
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	RXRA	chr1:85872768-85873521	SK-N-SH	brain:	n/a	chr1:85873385-85873404
2	EP300	chr1:85872632-85873370	SK-N-SH	brain:	n/a	chr1:85872787-85872796
3	JUND	chr1:85872681-85873321	SK-N-SH	brain:	n/a	chr1:85873017-85873028
4	POLR2A	chr1:85872687-85873353	HUVEC	blood vessel:	n/a	n/a
5	SP1	chr1:85872709-85873293	A549	lung:	n/a	n/a
6	ESR1	chr1:85872775-85873258	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr1:85872568-85873490	SK-N-SH	brain:	n/a	n/a
8	TCF12	chr1:85872588-85873479	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr1:85872803-85873300	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr1:85872728-85873364	ECC-1	luminal epithelium:	n/a	n/a
11	GATA3	chr1:85872755-85873345	SK-N-SH	brain:	n/a	n/a
12	PBX3	chr1:85872731-85873289	SK-N-SH	brain:	n/a	chr1:85872992-85873012
13	GATA3	chr1:85872696-85873530	SK-N-SH	brain:	n/a	chr1:85872751-85872761
14	ESR1	chr1:85872793-85873242	ECC-1	luminal epithelium:	n/a	n/a
15	NFIC	chr1:85872613-85873448	SK-N-SH	brain:	n/a	n/a
16	TEAD4	chr1:85872829-85873288	HCT-116	colon:	n/a	n/a
17	RXRA	chr1:85872783-85873394	SK-N-SH	brain:	n/a	n/a
18	ESR1	chr1:85872926-85873364	ECC-1	luminal epithelium:	n/a	n/a
19	ESR1	chr1:85872838-85873327	ECC-1	luminal epithelium:	n/a	n/a
20	STAT3	chr1:85872868-85873293	MCF10A-Er-Src	breast:	n/a	chr1:85873018-85873027 chr1:85873019-85873028
21	CBX3	chr1:85872768-85873303	HCT-116	colon:	n/a	n/a
22	JUND	chr1:85872684-85873398	SK-N-SH	brain:	n/a	chr1:85873017-85873028
23	NFIC	chr1:85872702-85873328	ECC-1	luminal epithelium:	n/a	n/a
24	EP300	chr1:85872810-85873258	SK-N-SH_RA	brain:	n/a	n/a
25	JUND	chr1:85872689-85873443	SK-N-SH	brain:	n/a	chr1:85873017-85873028
26	TCF12	chr1:85872695-85873256	A549	lung:	n/a	n/a
27	EP300	chr1:85872800-85873313	SK-N-SH_RA	brain:	n/a	n/a
28	NFIC	chr1:85872749-85873347	SK-N-SH	brain:	n/a	n/a
29	TCF12	chr1:85872650-85873293	ECC-1	luminal epithelium:	n/a	n/a
30	FOSL2	chr1:85872705-85873348	A549	lung:	n/a	n/a
31	EP300	chr1:85872641-85873451	ECC-1	luminal epithelium:	n/a	chr1:85873403-85873417 chr1:85872787-85872796
32	JUND	chr1:85872710-85873332	HCT-116	colon:	n/a	chr1:85873017-85873028
33	FOS	chr1:85872803-85873242	HUVEC	blood vessel:	n/a	chr1:85873017-85873028
34	PBX3	chr1:85872780-85873330	SK-N-SH	brain:	n/a	chr1:85872992-85873012
35	TEAD4	chr1:85872730-85873384	SK-N-SH	brain:	n/a	n/a
36	NFIC	chr1:85872691-85873420	ECC-1	luminal epithelium:	n/a	n/a
37	ESR1	chr1:85872739-85873381	ECC-1	luminal epithelium:	n/a	n/a
38	FOSL2	chr1:85872762-85873240	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85872823..85874492-chr1:85874813..85877121,2	MCF-7	breast:

Variant related genes	Relation type
DDAH1	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10158674	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[TSI][hapmap]
rs10782550	0.92[ASN][1000 genomes]
rs11161597	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161599	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161614	0.86[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs11161616	0.85[GIH][hapmap]
rs11161618	0.84[CHB][hapmap]
rs11801146	0.89[ASN][1000 genomes]
rs12067136	1.00[YRI][hapmap]
rs12118950	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120551	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12122816	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12123745	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125900	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12128907	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12129502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12130145	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12130380	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs12130591	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12131926	0.89[EUR][1000 genomes]
rs12132677	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135333	0.90[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12138621	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12138852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139958	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140170	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12140272	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12140457	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140935	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12403276	0.83[MKK][hapmap]
rs12405017	1.00[YRI][hapmap]
rs12717763	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12724823	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12736004	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12743049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12758237	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758768	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498374	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1608536	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384381	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17388521	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];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076699	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300639	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300640	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28529751	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34561661	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35193119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35240561	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35761966	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs36110608	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768223	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71652696	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3393958	chr1:85857980-85874598	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12133722	BCL10	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85862200-85874600	Weak transcription	Pancreas	Pancrea
2	chr1:85864400-85874600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:85864800-85876800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:85869800-85874400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:85870200-85874800	Enhancers	Osteobl	bone
6	chr1:85871400-85874000	Enhancers	HSMM	muscle
7	chr1:85871400-85878400	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:85871600-85876600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:85871800-85873600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:85871800-85877000	Weak transcription	Ovary	ovary
11	chr1:85872000-85877200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:85872400-85873600	Flanking Active TSS	HUVEC	blood vessel
13	chr1:85872400-85874000	Enhancers	Fetal Lung	lung
14	chr1:85872600-85873400	Enhancers	Adipose Nuclei	Adipose
15	chr1:85872600-85873800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:85872600-85873800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:85872600-85873800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:85872600-85874000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:85872800-85873400	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr1:85872800-85873400	Active TSS	Aorta	Aorta
21	chr1:85872800-85873400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:85872800-85873400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:85872800-85873400	Flanking Active TSS	NH-A	brain
24	chr1:85872800-85873400	Flanking Active TSS	NHEK	skin
25	chr1:85872800-85873600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:85872800-85873600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:85872800-85873800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:85872800-85873800	Flanking Active TSS	Liver	Liver
29	chr1:85872800-85873800	Enhancers	Fetal Intestine Small	intestine
30	chr1:85872800-85873800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr1:85872800-85874000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr1:85872800-85874200	Enhancers	Colon Smooth Muscle	Colon
33	chr1:85872800-85874400	Enhancers	Stomach Smooth Muscle	stomach
34	chr1:85872800-85874400	Enhancers	HepG2	liver
35	chr1:85872800-85874800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:85873000-85873400	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr1:85873000-85873400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr1:85873000-85873400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:85873000-85873400	Enhancers	HMEC	breast
40	chr1:85873000-85873400	Flanking Active TSS	HSMMtube	muscle
41	chr1:85873000-85873600	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr1:85873000-85873600	Enhancers	Fetal Intestine Large	intestine
43	chr1:85873000-85873600	Enhancers	Hela-S3	cervix
44	chr1:85873000-85873800	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr1:85873000-85873800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:85873000-85873800	Enhancers	Fetal Stomach	stomach
47	chr1:85873000-85875400	Enhancers	Brain Anterior Caudate	brain
48	chr1:85873200-85873400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:85873200-85873400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:85873200-85873400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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