Variant report

Variant	rs6490278
Chromosome Location	chr12:120428468-120428469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120427745..120429727-chr12:120729725..120731576,2	MCF-7	breast:
2	chr12:120426620..120429059-chr12:120727400..120730169,3	MCF-7	breast:
3	chr12:120427086..120431307-chr12:120435070..120439124,5	MCF-7	breast:
4	chr12:120425209..120429306-chr12:120552934..120555400,5	MCF-7	breast:
5	chr12:120428276..120430346-chr12:120637372..120639264,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089157	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000135127	Chromatin interaction
ENSG00000111737	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10128766	0.83[CHB][hapmap]
rs10400498	0.83[CHB][hapmap]
rs10744747	0.97[ASN][1000 genomes]
rs10849732	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs10849735	0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs10849736	0.83[CHB][hapmap]
rs11064986	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11064998	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065003	0.83[CHB][hapmap]
rs11065004	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11065014	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11065017	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11065018	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12310591	0.85[EUR][1000 genomes]
rs12311327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12320072	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12422923	0.84[EUR][1000 genomes]
rs2240311	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2393570	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2893812	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3742044	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759399	0.81[ASN][1000 genomes]
rs3852586	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3852588	0.80[ASN][1000 genomes]
rs3886910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3999575	0.81[ASN][1000 genomes]
rs4105713	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4351876	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767870	0.87[CHB][hapmap];0.98[ASN][1000 genomes]
rs4767873	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4767875	0.82[EUR][1000 genomes]
rs6490280	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6490281	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6490284	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7295717	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7298183	0.87[EUR][1000 genomes]
rs7302874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304325	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs7305625	0.83[EUR][1000 genomes]
rs7306739	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7312811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][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];0.99[ASN][1000 genomes]
rs7312971	0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs7314959	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7956436	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7958497	0.84[GIH][hapmap]
rs7960725	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7961738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7968557	0.82[CHB][hapmap]
rs7971249	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs7977281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978927	0.85[EUR][1000 genomes]
rs7980464	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510575	chr12:120303163-120437490	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3421380	chr12:120424669-120428967	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	esv3424419	chr12:120426069-120428817	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	esv3327583	chr12:120426194-120428742	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	esv1801020	chr12:120426469-120428468	Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv1833694	chr12:120426469-120428468	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	esv1836343	chr12:120426469-120428468	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv560408	chr12:120426469-120428468	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	esv1844134	chr12:120426469-120441443	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv1845761	chr12:120426469-120441443	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	esv3421881	chr12:120426594-120429142	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	esv1797666	chr12:120426666-120449259	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	esv1807589	chr12:120426666-120449259	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	esv1850441	chr12:120426820-120428468	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
18	nsv560424	chr12:120426820-120428468	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120426200-120428600	Active TSS	H9 Cell Line	embryonic stem cell
2	chr12:120426200-120429400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:120426400-120429000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:120426400-120429000	Active TSS	Esophagus	oesophagus
5	chr12:120427800-120428600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:120427800-120428600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:120427800-120428600	Flanking Active TSS	Brain Cingulate Gyrus	brain
8	chr12:120427800-120428600	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr12:120427800-120428600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr12:120427800-120428600	Flanking Active TSS	HMEC	breast
11	chr12:120427800-120428800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr12:120427800-120428800	Flanking Active TSS	Thymus	Thymus
13	chr12:120427800-120428800	Flanking Active TSS	NHEK	skin
14	chr12:120427800-120429400	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr12:120427800-120431000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:120428000-120428600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
17	chr12:120428000-120428600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:120428000-120428600	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:120428000-120428600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
20	chr12:120428000-120428600	Flanking Bivalent TSS/Enh	HepG2	liver
21	chr12:120428000-120428800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr12:120428000-120428800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr12:120428000-120429000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
24	chr12:120428000-120429000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr12:120428000-120429000	Flanking Active TSS	GM12878-XiMat	blood
26	chr12:120428000-120429000	Flanking Active TSS	Hela-S3	cervix
27	chr12:120428000-120429400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr12:120428000-120429600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:120428000-120432200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
30	chr12:120428200-120428600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:120428200-120428600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:120428200-120428600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
33	chr12:120428200-120428600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
34	chr12:120428200-120428600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
35	chr12:120428200-120428600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
36	chr12:120428200-120428600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
37	chr12:120428200-120428600	Enhancers	Primary hematopoietic stem cells	blood
38	chr12:120428200-120428600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
39	chr12:120428200-120428600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:120428200-120428600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr12:120428200-120428600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:120428200-120428600	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr12:120428200-120428600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
44	chr12:120428200-120428600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
45	chr12:120428200-120428600	Flanking Active TSS	Dnd41	blood
46	chr12:120428200-120428800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
47	chr12:120428200-120428800	Enhancers	Primary B cells from peripheral blood	blood
48	chr12:120428200-120428800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr12:120428200-120428800	Flanking Active TSS	Fetal Brain Female	brain
50	chr12:120428200-120428800	Enhancers	Rectal Mucosa Donor 31	rectum

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