Variant report

Variant	rs7964495
Chromosome Location	chr12:46156701-46156702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46122273..46123989-chr12:46154776..46157758,3	MCF-7	breast:
2	chr12:46149877..46152600-chr12:46155145..46158037,2	K562	blood:
3	chr12:46119651..46123075-chr12:46155146..46159622,5	MCF-7	breast:
4	chr12:46156094..46158266-chr12:46298967..46301414,2	MCF-7	breast:
5	chr12:46156363..46159128-chr12:46168846..46171397,2	K562	blood:
6	chr12:46122681..46123305-chr12:46156413..46157018,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273015	Chromatin interaction
ENSG00000189079	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10161001	1.00[EUR][1000 genomes]
rs10161062	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs10161510	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10161536	1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[YRI][hapmap]
rs10880858	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs11183108	1.00[EUR][1000 genomes]
rs11183109	1.00[EUR][1000 genomes]
rs11183135	1.00[EUR][1000 genomes]
rs11183136	1.00[EUR][1000 genomes]
rs11183171	1.00[MEX][hapmap]
rs11183197	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11183199	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11183202	0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11183248	0.80[YRI][hapmap]
rs11574971	1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[YRI][hapmap]
rs12296933	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs12297214	0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12298597	1.00[EUR][1000 genomes]
rs12299715	1.00[EUR][1000 genomes]
rs12301665	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12302862	0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12305110	1.00[EUR][1000 genomes]
rs12309988	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs12312478	1.00[EUR][1000 genomes]
rs12313957	1.00[EUR][1000 genomes]
rs12316100	1.00[EUR][1000 genomes]
rs12316361	0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs12316726	1.00[EUR][1000 genomes]
rs12321106	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28583490	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4522236	1.00[EUR][1000 genomes]
rs55916269	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56338250	1.00[EUR][1000 genomes]
rs58253063	1.00[EUR][1000 genomes]
rs59027429	1.00[EUR][1000 genomes]
rs59340060	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6582560	1.00[EUR][1000 genomes]
rs6582575	1.00[CHD][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs7132585	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7133123	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs7296694	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs7303119	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7308856	0.85[ASW][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7308893	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs7309921	0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7310702	0.83[YRI][hapmap]
rs7315365	1.00[EUR][1000 genomes]
rs74081382	1.00[EUR][1000 genomes]
rs74081384	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74081401	1.00[EUR][1000 genomes]
rs74084208	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7953515	1.00[EUR][1000 genomes]
rs7965539	0.86[YRI][hapmap]
rs7971936	1.00[CHD][hapmap]
rs7972650	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs7973967	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7975170	0.85[ASW][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7975408	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs7977711	1.00[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	nsv899052	chr12:46068394-46175469	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
2	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv973961	chr12:46153815-46175394	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv832396	chr12:46155424-46310583	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46125000-46161200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:46126400-46161200	Weak transcription	Aorta	Aorta
3	chr12:46127200-46161200	Weak transcription	HMEC	breast
4	chr12:46128200-46164600	Weak transcription	Esophagus	oesophagus
5	chr12:46131200-46160800	Weak transcription	NHEK	skin
6	chr12:46132000-46161800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:46132000-46205200	Weak transcription	HSMM	muscle
8	chr12:46132200-46165000	Weak transcription	Lung	lung
9	chr12:46136400-46159400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:46136600-46157800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:46137400-46160800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:46137400-46163000	Weak transcription	Fetal Intestine Large	intestine
13	chr12:46137400-46174400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:46137600-46161800	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:46141000-46161800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:46142000-46168400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:46142200-46161200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:46143600-46161400	Weak transcription	Thymus	Thymus
19	chr12:46145400-46167600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:46145600-46157200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:46145600-46158200	Weak transcription	Primary T cells from cord blood	blood
22	chr12:46146600-46161200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:46147000-46161200	Weak transcription	Left Ventricle	heart
24	chr12:46148200-46160800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:46148400-46168200	Weak transcription	Psoas Muscle	Psoas
26	chr12:46148600-46164000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr12:46149200-46162000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:46149600-46215400	Weak transcription	Fetal Kidney	kidney
29	chr12:46150200-46158600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:46150200-46162200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:46150600-46157200	Weak transcription	Right Atrium	heart
32	chr12:46150600-46161200	Weak transcription	Fetal Thymus	thymus
33	chr12:46150600-46161400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:46150600-46162000	Weak transcription	Fetal Intestine Small	intestine
35	chr12:46150600-46163600	Weak transcription	Fetal Stomach	stomach
36	chr12:46151200-46161200	Weak transcription	Right Ventricle	heart
37	chr12:46151200-46161200	Weak transcription	GM12878-XiMat	blood
38	chr12:46151200-46162200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:46151400-46159400	Weak transcription	Dnd41	blood
40	chr12:46151400-46162200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr12:46151400-46168800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:46151400-46169800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr12:46151600-46158200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:46151600-46162600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:46152400-46160800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr12:46152600-46161400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:46152600-46162000	Weak transcription	Primary B cells from cord blood	blood
48	chr12:46153800-46164400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:46155200-46156800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:46155800-46156800	Enhancers	Primary T helper cells PMA-I stimulated	--

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