Variant report

Variant	rs2292657
Chromosome Location	chr12:57859932-57859933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57858770..57860862-chr12:57912949..57914502,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10783826	0.94[ASN][1000 genomes]
rs10783828	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876986	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876987	0.99[ASN][1000 genomes]
rs11544238	0.96[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2228224	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2228225	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2228226	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277315	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277316	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277317	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277318	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3782125	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3782126	0.84[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3817474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3817475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3825077	0.90[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4760148	0.83[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4760255	0.85[AMR][1000 genomes]
rs4760259	0.80[CEU][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs7309467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv8974	chr12:57852779-57865881	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	n/a
14	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57856200-57863200	Weak transcription	Gastric	stomach
2	chr12:57856600-57860600	Weak transcription	Primary T cells from cord blood	blood
3	chr12:57856600-57863200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:57856600-57865800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:57856800-57861000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr12:57856800-57861000	Weak transcription	Thymus	Thymus
7	chr12:57856800-57861000	Weak transcription	Spleen	Spleen
8	chr12:57856800-57863000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:57856800-57863000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:57856800-57863800	Weak transcription	Fetal Kidney	kidney
11	chr12:57856800-57864400	Weak transcription	Liver	Liver
12	chr12:57856800-57864800	Strong transcription	Fetal Lung	lung
13	chr12:57856800-57865000	Weak transcription	Brain Substantia Nigra	brain
14	chr12:57856800-57865600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:57856800-57866200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:57857000-57861000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:57857000-57861200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:57857000-57861200	Weak transcription	Fetal Thymus	thymus
19	chr12:57857000-57861400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:57857000-57861800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:57857000-57862800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:57857000-57862800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:57857000-57863000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:57857000-57863000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:57857000-57863000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:57857000-57863000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:57857000-57863000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:57857000-57863200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:57857000-57864200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:57857000-57865800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:57857000-57868400	Weak transcription	Dnd41	blood
32	chr12:57857000-57869400	Weak transcription	Ovary	ovary
33	chr12:57857200-57860600	Weak transcription	Primary B cells from cord blood	blood
34	chr12:57857200-57862800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:57857200-57866200	Strong transcription	Fetal Stomach	stomach
36	chr12:57857400-57865800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:57857800-57865400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:57858000-57861800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr12:57858000-57863000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:57858000-57863000	Strong transcription	Fetal Intestine Small	intestine
41	chr12:57858200-57861400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:57858400-57860000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:57858600-57861000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:57858600-57861400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr12:57858600-57864400	Weak transcription	Colonic Mucosa	Colon
46	chr12:57858800-57860800	Weak transcription	GM12878-XiMat	blood
47	chr12:57859400-57860000	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr12:57859400-57860200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:57859400-57860200	Enhancers	K562	blood
50	chr12:57859400-57861000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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