Variant report

Variant	rs7972499
Chromosome Location	chr12:46381265-46381266
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46381030..46386260-chr12:46762457..46768592,6	K562	blood:
2	chr12:46344593..46346817-chr12:46380170..46382084,2	MCF-7	breast:
3	chr12:46234148..46236211-chr12:46380444..46382756,2	MCF-7	breast:
4	chr12:46117578..46127110-chr12:46379884..46387671,22	K562	blood:
5	chr12:46119117..46128831-chr12:46378175..46388065,20	MCF-7	breast:
6	chr12:46121142..46128895-chr12:46378215..46381675,6	K562	blood:
7	chr12:46014914..46017037-chr12:46380285..46382180,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273015	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000189079	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10161062	0.90[YRI][hapmap]
rs10161510	0.82[YRI][hapmap]
rs10161536	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506264	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10880858	0.93[YRI][hapmap]
rs11183248	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574971	0.92[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12296933	0.93[YRI][hapmap]
rs12298184	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12307979	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12309988	0.93[YRI][hapmap]
rs12314576	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1549591	1.00[EUR][1000 genomes]
rs15852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17096316	1.00[EUR][1000 genomes]
rs61009645	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6582575	0.93[YRI][hapmap]
rs6582580	1.00[EUR][1000 genomes]
rs7133123	0.93[YRI][hapmap]
rs7296694	1.00[YRI][hapmap]
rs7304785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7306774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7310702	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74081279	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74081280	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74081611	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7965539	0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7970212	1.00[EUR][1000 genomes]
rs7970367	1.00[EUR][1000 genomes]
rs7971936	1.00[EUR][1000 genomes]
rs7973967	0.81[YRI][hapmap]
rs7975408	0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv983463	chr12:46377328-46403983	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers 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	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46360600-46381400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:46360600-46381800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr12:46360600-46383000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:46361400-46383200	Weak transcription	Lung	lung
5	chr12:46362800-46383400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:46363600-46381800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:46367400-46383200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:46370800-46382800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:46372400-46383000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:46373000-46383400	Weak transcription	Esophagus	oesophagus
11	chr12:46373200-46382800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr12:46374200-46383000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr12:46375600-46381400	Weak transcription	HUVEC	blood vessel
14	chr12:46378200-46381600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:46378400-46381400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:46378400-46382800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr12:46378400-46383000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr12:46378600-46382400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr12:46378600-46382600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:46379000-46381400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
21	chr12:46379000-46381800	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr12:46379000-46382400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:46379200-46381400	Weak transcription	Right Atrium	heart
24	chr12:46379400-46383000	Enhancers	Primary B cells from peripheral blood	blood
25	chr12:46379600-46381400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:46379600-46381600	Genic enhancers	K562	blood
27	chr12:46379600-46383000	Enhancers	Colon Smooth Muscle	Colon
28	chr12:46379800-46381800	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr12:46379800-46381800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr12:46380000-46382200	Enhancers	Liver	Liver
31	chr12:46380000-46382200	Enhancers	Brain Angular Gyrus	brain
32	chr12:46380000-46382600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr12:46380000-46383400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr12:46380200-46381400	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr12:46380200-46381400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:46380200-46381400	Weak transcription	Colonic Mucosa	Colon
37	chr12:46380200-46381400	Enhancers	Hela-S3	cervix
38	chr12:46380200-46381600	Genic enhancers	A549	lung
39	chr12:46380200-46381800	Enhancers	NHLF	lung
40	chr12:46380200-46382200	Enhancers	Thymus	Thymus
41	chr12:46380400-46383000	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr12:46380600-46381400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:46380600-46381400	Genic enhancers	Brain Hippocampus Middle	brain
44	chr12:46380600-46381400	Genic enhancers	Fetal Lung	lung
45	chr12:46380600-46381400	Genic enhancers	HMEC	breast
46	chr12:46380600-46381400	Genic enhancers	HSMM	muscle
47	chr12:46380600-46381400	Genic enhancers	NHEK	skin
48	chr12:46380600-46381600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:46380600-46381600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr12:46380600-46381600	Enhancers	Spleen	Spleen

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