Variant report

Variant	rs4108249
Chromosome Location	chr12:45744402-45744403
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	chr12:45734789..45737221-chr12:45742624..45745362,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12580320	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs12580810	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs1316777	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1316778	0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2081592	0.95[AFR][1000 genomes]
rs2162321	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3847983	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3847984	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4108250	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes]
rs55708540	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs55812173	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56408748	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57858655	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58221634	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58409854	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58824383	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs59436840	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs59728495	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs59789543	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs60011223	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs60287166	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs60457106	0.97[AFR][1000 genomes]
rs60831882	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61265799	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61349051	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7134442	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7294399	0.97[AFR][1000 genomes]
rs7299229	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7305478	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs74080812	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs74080813	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs74080816	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs74080818	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs74080819	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs74080820	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs74080826	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs74080830	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs74080831	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs74080884	0.97[AFR][1000 genomes]
rs7956153	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7960365	0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7969594	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7969966	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7970586	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7971106	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7974971	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7975088	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr12:45699800-45747800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:45723800-45757000	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:45725800-45782000	Weak transcription	Brain Angular Gyrus	brain
4	chr12:45726600-45747200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:45734600-45747600	Weak transcription	Stomach Mucosa	stomach
6	chr12:45735400-45755200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:45737400-45748800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:45738800-45754600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:45739000-45756000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr12:45739200-45752000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:45739800-45746600	Strong transcription	Primary T cells from cord blood	blood
12	chr12:45740000-45747800	Strong transcription	Fetal Thymus	thymus
13	chr12:45740400-45745600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:45740400-45745600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:45740400-45745800	Strong transcription	Left Ventricle	heart
16	chr12:45740400-45746000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:45740400-45746200	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:45740400-45746200	Strong transcription	Fetal Muscle Leg	muscle
19	chr12:45740400-45746600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr12:45740400-45747200	Strong transcription	Fetal Intestine Large	intestine
21	chr12:45740400-45755000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:45740600-45745400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
23	chr12:45740600-45745600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:45740600-45745600	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:45740600-45745800	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:45740600-45746000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:45740600-45746200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr12:45740800-45745800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr12:45740800-45748200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:45740800-45757600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:45741000-45752000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:45741400-45745600	Strong transcription	HMEC	breast
33	chr12:45741400-45755400	Weak transcription	Brain Anterior Caudate	brain
34	chr12:45741600-45745200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:45741600-45745200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:45741600-45745200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:45741800-45745200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:45741800-45745200	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr12:45741800-45745200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:45741800-45745200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr12:45741800-45745400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:45741800-45745600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:45741800-45745600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr12:45741800-45745600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:45741800-45745600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:45741800-45745600	Strong transcription	Fetal Kidney	kidney
47	chr12:45741800-45745800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:45741800-45745800	Strong transcription	Liver	Liver
49	chr12:45741800-45746000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:45741800-45746800	Strong transcription	Fetal Lung	lung

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