Variant report

Variant	rs670541
Chromosome Location	chr12:121569634-121569635
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	GATA3	chr12:121569540-121570286	MCF-7	breast:	n/a	chr12:121569900-121569908
2	JUN	chr12:121569328-121571628	K562	blood:	n/a	chr12:121571251-121571261 chr12:121571252-121571260 chr12:121571251-121571261 chr12:121571251-121571261 chr12:121571251-121571261
3	SIN3AK20	chr12:121569499-121570202	MCF-7	breast:	n/a	n/a
4	KAP1	chr12:121569281-121570057	U2OS	brain:	n/a	n/a
5	GATA3	chr12:121569512-121570382	MCF-7	breast:	n/a	chr12:121569900-121569908

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121569572..121570160-chr12:121640475..121641223,2	MCF-7	breast:
2	chr12:121550877..121553101-chr12:121566808..121569789,2	MCF-7	breast:

Variant related genes	Relation type
P2RX7	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12810503	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12813980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12816966	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12817169	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12819523	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs12819930	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12820593	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12824585	0.87[EUR][1000 genomes]
rs12830584	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12832396	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1718153	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17432871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17434640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17525809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs1794899	1.00[MEX][hapmap]
rs1796415	0.82[MKK][hapmap]
rs208302	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2260138	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2393752	0.97[ASN][1000 genomes]
rs2393753	0.85[ASN][1000 genomes]
rs2393754	0.88[ASN][1000 genomes]
rs2464844	0.82[ASN][1000 genomes]
rs2686372	1.00[CHB][hapmap]
rs28969465	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28969469	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34185850	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34449339	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34480856	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34572498	0.91[ASN][1000 genomes]
rs34805626	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35018823	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35076950	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35158421	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35237790	0.83[EUR][1000 genomes]
rs35455367	0.84[ASN][1000 genomes]
rs35579189	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35605477	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35760636	0.97[ASN][1000 genomes]
rs35869834	0.94[ASN][1000 genomes]
rs36133237	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs494986	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs513113	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs514109	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56098349	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs583187	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs585847	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs588130	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs588510	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs588573	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs599785	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs601636	0.91[ASN][1000 genomes]
rs603505	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603891	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs618201	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs657172	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66570654	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66811517	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs675718	0.97[ASN][1000 genomes]
rs676632	0.97[ASN][1000 genomes]
rs67691679	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67739439	0.90[ASN][1000 genomes]
rs67881993	0.97[ASN][1000 genomes]
rs71454676	0.94[ASN][1000 genomes]
rs71454679	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71454680	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73216114	0.94[ASN][1000 genomes]
rs73218241	0.91[ASN][1000 genomes]
rs934353	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs934354	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs934355	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv430537	chr12:121487632-121579955	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv899563	chr12:121543011-121600529	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121562400-121570600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:121562800-121570400	Weak transcription	Ovary	ovary
3	chr12:121564200-121570600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:121565800-121570600	Enhancers	Placenta	Placenta
5	chr12:121566600-121570200	Weak transcription	Small Intestine	intestine
6	chr12:121566800-121570400	Weak transcription	Gastric	stomach
7	chr12:121567000-121570200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:121567200-121569800	Weak transcription	NHEK	skin
9	chr12:121567200-121570000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:121567200-121570400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:121567200-121570400	Weak transcription	Fetal Lung	lung
12	chr12:121567200-121570400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:121567200-121570400	Weak transcription	HMEC	breast
14	chr12:121567400-121570400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:121567400-121570400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:121567400-121570400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:121567600-121569800	Enhancers	Brain Angular Gyrus	brain
18	chr12:121567600-121569800	Weak transcription	Fetal Intestine Small	intestine
19	chr12:121567600-121570000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:121567600-121570000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:121567600-121570000	Enhancers	Brain Substantia Nigra	brain
22	chr12:121567600-121570200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:121567600-121570200	Weak transcription	Fetal Heart	heart
24	chr12:121567600-121570200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:121567600-121570200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:121567600-121570400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:121567600-121570400	Enhancers	Primary T cells fromperipheralblood	blood
28	chr12:121567600-121570400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:121567600-121570400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr12:121567600-121570400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr12:121567600-121570400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr12:121567600-121570400	Weak transcription	Psoas Muscle	Psoas
33	chr12:121567600-121570400	Weak transcription	Right Atrium	heart
34	chr12:121567600-121570400	Weak transcription	Right Ventricle	heart
35	chr12:121567600-121570400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:121567600-121570400	Weak transcription	Stomach Mucosa	stomach
37	chr12:121567600-121570400	Weak transcription	NHDF-Ad	bronchial
38	chr12:121567600-121570600	Enhancers	Primary hematopoietic stem cells	blood
39	chr12:121567600-121570600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:121567600-121570600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:121567800-121569800	Enhancers	Brain Anterior Caudate	brain
42	chr12:121567800-121569800	Enhancers	Brain Cingulate Gyrus	brain
43	chr12:121567800-121570000	Enhancers	Brain Hippocampus Middle	brain
44	chr12:121567800-121570200	Weak transcription	Adipose Nuclei	Adipose
45	chr12:121567800-121570200	Weak transcription	Spleen	Spleen
46	chr12:121567800-121570200	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr12:121567800-121570400	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr12:121567800-121570400	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr12:121567800-121570400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:121567800-121570400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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