Variant report

Variant	rs11609875
Chromosome Location	chr12:122608502-122608503
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	CTCF	chr12:122608500-122608650	HEK293	kidney:	n/a	n/a
2	CTCF	chr12:122608400-122608550	HBMEC	blood vessel:	n/a	n/a
3	CTCF	chr12:122607537-122608515	A549	lung:	n/a	chr12:122607920-122607936 chr12:122607914-122607935 chr12:122607919-122607937
4	CTCF	chr12:122608380-122608530	HBMEC	blood vessel:	n/a	n/a
5	RAD21	chr12:122607330-122608595	SK-N-SH	brain:	n/a	chr12:122607917-122607936 chr12:122608467-122608480
6	SMC3	chr12:122607389-122608651	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr12:122608440-122608590	GM12872	blood:	n/a	n/a
8	CTCF	chr12:122607523-122608684	SK-N-SH	brain:	n/a	chr12:122607920-122607936 chr12:122607914-122607935 chr12:122607919-122607937
9	CTCF	chr12:122608360-122608510	GM12871	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122607579..122610037-chr12:122611336..122613459,2	MCF-7	breast:
2	chr12:122515031..122519836-chr12:122606166..122610448,7	MCF-7	breast:
3	chr12:122492019..122492888-chr12:122608485..122609005,2	MCF-7	breast:
4	chr12:122601261..122606063-chr12:122607168..122609213,4	K562	blood:
5	chr12:122491907..122493455-chr12:122607305..122608643,21	MCF-7	breast:
6	chr12:122584007..122585799-chr12:122606891..122609136,2	K562	blood:
7	chr12:122492379..122495152-chr12:122604029..122610434,5	MCF-7	breast:

Variant related genes	Relation type
MLXIP	TF binding region
ENSG00000175727	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1047796	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1047813	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10744177	0.87[EUR][1000 genomes]
rs10744335	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10770189	0.80[EUR][1000 genomes]
rs10773037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846525	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11057184	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11057654	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057905	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11059094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11060477	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061156	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11061602	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11608788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11608792	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835818	0.83[EUR][1000 genomes]
rs12366611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1976859	0.82[EUR][1000 genomes]
rs2280573	0.82[EUR][1000 genomes]
rs2280574	0.82[EUR][1000 genomes]
rs28385906	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28401575	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28410367	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28414202	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28421373	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28430881	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28450064	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28453771	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28461580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28464252	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28478366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28478717	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28498002	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28498376	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28503672	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28506952	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28517281	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28529535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28530689	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28545660	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28548845	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28569273	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28580546	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28585613	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28591322	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28605425	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28607028	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28613772	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28626850	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28629903	0.85[EUR][1000 genomes]
rs28631172	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28639626	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28642975	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28649184	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28652632	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28683032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28691281	0.82[EUR][1000 genomes]
rs28699616	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28737311	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28739522	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28759327	0.82[EUR][1000 genomes]
rs34047484	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34123446	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34439774	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34532891	0.92[EUR][1000 genomes]
rs34741056	0.91[EUR][1000 genomes]
rs34974633	0.92[EUR][1000 genomes]
rs35159488	0.80[EUR][1000 genomes]
rs35249105	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35676267	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35764187	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36079122	0.88[EUR][1000 genomes]
rs3809117	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3892367	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4758653	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4758654	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4758685	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4758686	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4758687	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4758688	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4758690	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4758691	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56072019	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61952902	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61952904	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61952920	0.89[EUR][1000 genomes]
rs61952922	0.94[EUR][1000 genomes]
rs61952923	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6489238	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6489242	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6489244	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7137049	0.82[EUR][1000 genomes]
rs7312210	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73217796	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7484733	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7485054	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7485380	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7485447	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7486198	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7487292	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7487608	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7488268	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7488393	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7488857	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7953704	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7955571	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7955575	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7962500	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7964148	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7967127	0.86[EUR][1000 genomes]
rs7975001	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899569	chr12:122478728-122630909	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS 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	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122583200-122612200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:122584200-122622000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:122592200-122611800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:122599000-122614400	Weak transcription	Fetal Kidney	kidney
5	chr12:122599200-122612200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:122600600-122612400	Weak transcription	Aorta	Aorta
7	chr12:122603200-122610000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:122604400-122611200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr12:122604800-122608600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:122605200-122608600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:122605200-122608600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:122605200-122608600	Enhancers	Ovary	ovary
13	chr12:122605200-122608600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr12:122605400-122608600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr12:122605800-122608600	Enhancers	Colonic Mucosa	Colon
16	chr12:122606000-122608600	Enhancers	Adipose Nuclei	Adipose
17	chr12:122606000-122608800	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr12:122606200-122608600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr12:122606200-122608600	Genic enhancers	Fetal Intestine Small	intestine
20	chr12:122606200-122608600	Genic enhancers	Fetal Stomach	stomach
21	chr12:122606200-122608600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr12:122606400-122608600	Enhancers	Primary T cells from cord blood	blood
23	chr12:122606400-122611200	Enhancers	Fetal Muscle Leg	muscle
24	chr12:122607200-122610800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr12:122607400-122608600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:122607400-122608600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr12:122607400-122608600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:122607400-122608600	Enhancers	Esophagus	oesophagus
29	chr12:122607400-122608600	Enhancers	Fetal Intestine Large	intestine
30	chr12:122607400-122608600	Enhancers	Pancreas	Pancrea
31	chr12:122607400-122608600	Enhancers	Right Atrium	heart
32	chr12:122607400-122611600	Enhancers	Liver	Liver
33	chr12:122607600-122608600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:122607600-122608600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:122607600-122608600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:122607600-122608600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:122607600-122608600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:122607600-122608600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:122607600-122608600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:122607600-122608600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr12:122607600-122608600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:122607600-122608600	Genic enhancers	Muscle Satellite Cultured Cells	--
43	chr12:122607600-122608600	Enhancers	Brain Substantia Nigra	brain
44	chr12:122607600-122608600	Enhancers	Right Ventricle	heart
45	chr12:122607600-122608600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr12:122607600-122608600	Enhancers	Stomach Mucosa	stomach
47	chr12:122607600-122608600	Enhancers	HMEC	breast
48	chr12:122607600-122608600	Genic enhancers	K562	blood
49	chr12:122607600-122608600	Enhancers	NH-A	brain
50	chr12:122607600-122608600	Enhancers	NHDF-Ad	bronchial

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