Variant report

Variant	rs12475684
Chromosome Location	chr2:32609993-32609994
allele	C/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	chr2:32609914-32611002	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:32609033-32610235	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:32609490-32610012	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:32582832..32585768-chr2:32608002..32610374,2	K562	blood:
2	chr2:32609238..32611905-chr2:32621057..32622626,2	MCF-7	breast:

Variant related genes	Relation type
BIRC6	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1046602	0.89[EUR][1000 genomes]
rs12470811	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470951	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011943	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011947	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011963	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35368935	0.89[EUR][1000 genomes]
rs36060675	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41291167	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952257	0.84[EUR][1000 genomes]
rs4952259	0.91[EUR][1000 genomes]
rs4952260	0.89[EUR][1000 genomes]
rs55788900	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56347254	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57813560	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61439415	0.82[EUR][1000 genomes]
rs62134039	0.80[EUR][1000 genomes]
rs62134043	0.84[EUR][1000 genomes]
rs62134044	0.84[EUR][1000 genomes]
rs62134045	0.82[EUR][1000 genomes]
rs62134050	0.89[EUR][1000 genomes]
rs62134052	0.89[EUR][1000 genomes]
rs62134054	0.89[EUR][1000 genomes]
rs62134059	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136263	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136264	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136269	1.00[ASN][1000 genomes]
rs62136276	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136278	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136279	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136280	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136281	1.00[ASN][1000 genomes]
rs62136282	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136284	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136285	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136286	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136287	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136302	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136306	1.00[ASN][1000 genomes]
rs62136326	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136348	1.00[ASN][1000 genomes]
rs6543655	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747906	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72798728	0.84[EUR][1000 genomes]
rs72798733	0.87[EUR][1000 genomes]
rs72798777	1.00[ASN][1000 genomes]
rs72798784	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72798788	1.00[ASN][1000 genomes]
rs72798796	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800830	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609320	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv2422335	chr2:32412330-33200581	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv533153	chr2:32514528-33249136	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	esv2751888	chr2:32539236-33331549	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv516173	chr2:32541438-33329957	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	esv2763243	chr2:32567339-33331778	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32583600-32623000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:32583600-32653200	Weak transcription	Gastric	stomach
3	chr2:32583800-32649000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:32601000-32611600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:32602000-32617400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:32602000-32653000	Weak transcription	Stomach Mucosa	stomach
7	chr2:32602400-32618600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:32603200-32617200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:32603200-32617200	Weak transcription	Right Ventricle	heart
10	chr2:32603200-32620600	Weak transcription	Fetal Brain Male	brain
11	chr2:32603400-32610600	Weak transcription	Aorta	Aorta
12	chr2:32603400-32616600	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:32603400-32617200	Weak transcription	Small Intestine	intestine
14	chr2:32603400-32620800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:32604600-32618800	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:32604600-32624000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:32604600-32635000	Strong transcription	Fetal Thymus	thymus
18	chr2:32604600-32635200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:32604600-32637200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:32604800-32635600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:32605000-32616600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:32605200-32612400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:32605200-32613000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:32605200-32614400	Strong transcription	Dnd41	blood
25	chr2:32605200-32615000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:32605200-32615800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:32605200-32622600	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr2:32605200-32624800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:32605200-32635400	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr2:32605200-32637200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:32605400-32615600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr2:32605400-32615800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:32605400-32621400	Weak transcription	Colonic Mucosa	Colon
34	chr2:32605400-32622600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:32605400-32623400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:32605400-32625200	Strong transcription	Fetal Intestine Large	intestine
37	chr2:32605400-32652800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:32605600-32613000	Strong transcription	Osteobl	bone
39	chr2:32605600-32615200	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:32605600-32615600	Strong transcription	Thymus	Thymus
41	chr2:32605600-32624800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:32605800-32614800	Strong transcription	GM12878-XiMat	blood
43	chr2:32605800-32615400	Strong transcription	Adipose Nuclei	Adipose
44	chr2:32605800-32634000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr2:32606000-32623600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr2:32606200-32610000	Strong transcription	Fetal Stomach	stomach
47	chr2:32606200-32622600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:32606400-32610000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:32606800-32612400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:32606800-32612800	Strong transcription	Primary T cells from cord blood	blood

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