Variant report

Variant	rs57529731
Chromosome Location	chr12:11707435-11707436
allele	A/G
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	POLR2A	chr12:11706778-11710160	GM12891	blood:	n/a	n/a
2	POLR2A	chr12:11706837-11708074	GM12891	blood:	n/a	n/a
3	CTCF	chr12:11706643-11707978	A549	lung:	n/a	chr12:11707059-11707075 chr12:11707058-11707076 chr12:11707060-11707081
4	SMC3	chr12:11706733-11707694	GM12878	blood:	n/a	chr12:11707060-11707074
5	ESRRA	chr12:11706292-11707738	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:11706813-11709512	GM12878	blood:	n/a	n/a
7	CTCF	chr12:11707380-11707530	BE2_C	brain:	n/a	n/a
8	SMC3	chr12:11706791-11707937	SK-N-SH	brain:	n/a	chr12:11707060-11707074
9	POLR2A	chr12:11706788-11707468	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:11706703-11707542	GM12878	blood:	n/a	n/a
11	CHD1	chr12:11706945-11707941	GM12878	blood:	n/a	n/a
12	MXI1	chr12:11706567-11707494	GM12878	blood:	n/a	n/a
13	MXI1	chr12:11706678-11707874	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr12:11706497-11707534	SK-N-SH	brain:	n/a	chr12:11707059-11707075 chr12:11707058-11707076 chr12:11707060-11707081
15	STAT3	chr12:11706816-11707752	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10923458..10924277-chr12:11707052..11707592,2	K562	blood:
2	chr12:11706600..11707499-chr12:12186007..12186739,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247157	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10491979	0.93[EUR][1000 genomes]
rs10491981	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304175	0.96[EUR][1000 genomes]
rs12307843	0.93[EUR][1000 genomes]
rs16935010	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16935013	1.00[EUR][1000 genomes]
rs16935135	0.96[EUR][1000 genomes]
rs17745379	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745415	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17818016	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17818022	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795551	0.97[EUR][1000 genomes]
rs61472986	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302311	0.93[EUR][1000 genomes]
rs73286605	0.93[EUR][1000 genomes]
rs73286618	0.96[EUR][1000 genomes]
rs7954816	0.93[EUR][1000 genomes]
rs7972594	0.93[EUR][1000 genomes]
rs7975032	0.90[EUR][1000 genomes]
rs969769	0.93[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	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv469112	chr12:11575570-11711690	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv557573	chr12:11575570-11711690	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11697400-11708600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:11699000-11709000	Weak transcription	Fetal Lung	lung
3	chr12:11706400-11708600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:11706600-11708600	Enhancers	Primary T cells from cord blood	blood
5	chr12:11706800-11707600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr12:11706800-11707600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr12:11706800-11707600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr12:11706800-11707600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr12:11706800-11707600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:11706800-11707600	Active TSS	Aorta	Aorta
11	chr12:11706800-11707600	Enhancers	Fetal Thymus	thymus
12	chr12:11706800-11707800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:11706800-11707800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:11706800-11707800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr12:11706800-11708200	Enhancers	Stomach Smooth Muscle	stomach
16	chr12:11706800-11708600	Enhancers	Colon Smooth Muscle	Colon
17	chr12:11706800-11708600	Enhancers	Rectal Smooth Muscle	rectum
18	chr12:11706800-11708800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:11706800-11708800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:11706800-11709400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:11706800-11709600	Enhancers	Dnd41	blood
22	chr12:11707200-11707600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr12:11707200-11707600	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr12:11707200-11707600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:11707200-11707600	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr12:11707200-11707800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr12:11707200-11707800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr12:11707200-11708000	Flanking Active TSS	GM12878-XiMat	blood
29	chr12:11707200-11708400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:11707200-11708400	Weak transcription	Stomach Mucosa	stomach
31	chr12:11707200-11708600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr12:11707200-11708600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:11707200-11708600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:11707400-11708000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:11707400-11708400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:11707400-11708400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:11707400-11708400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:11707400-11708400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr12:11707400-11708400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr12:11707400-11708600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:11707400-11708600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:11707400-11708800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:11707400-11708800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:11707400-11709000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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