Variant report

Variant	rs1316778
Chromosome Location	chr12:45740993-45740994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:45737306..45740256-chr12:45740506..45742097,2	MCF-7	breast:
2	chr12:45736486..45738721-chr12:45739577..45741327,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARID2-9	chr12:45740805-45741291	NONHSAT027825

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

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

rs_ID	r²[population]
rs12580320	0.85[YRI][hapmap];1.00[AFR][1000 genomes]
rs12580810	0.85[YRI][hapmap];1.00[AFR][1000 genomes]
rs1316777	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2081592	0.98[AFR][1000 genomes]
rs2162321	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3847983	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3847984	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4108249	0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4108250	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs55708540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55812173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56408748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57858655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58221634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58409854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58824383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59436840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59728495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59789543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60011223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60287166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60457106	1.00[AFR][1000 genomes]
rs60831882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61265799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61349051	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7134442	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7294399	1.00[AFR][1000 genomes]
rs7299229	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7305478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080884	1.00[AFR][1000 genomes]
rs7956153	0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7960365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7969594	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7969966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7970586	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7971106	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7974971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7975088	1.00[AFR][1000 genomes];1.00[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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45693000-45744000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:45695200-45741800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr12:45698000-45744400	Weak transcription	Fetal Brain Male	brain
4	chr12:45699000-45741800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr12:45699800-45747800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:45700000-45743600	Weak transcription	Gastric	stomach
7	chr12:45701400-45743400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:45708600-45742000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:45709200-45743600	Weak transcription	Spleen	Spleen
10	chr12:45709800-45741800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:45709800-45743800	Weak transcription	Fetal Stomach	stomach
12	chr12:45710200-45741800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:45710400-45741400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:45720600-45741800	Weak transcription	Pancreas	Pancrea
15	chr12:45720600-45743600	Weak transcription	Lung	lung
16	chr12:45720800-45741800	Weak transcription	Small Intestine	intestine
17	chr12:45722200-45744400	Weak transcription	Esophagus	oesophagus
18	chr12:45723800-45757000	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:45725800-45782000	Weak transcription	Brain Angular Gyrus	brain
20	chr12:45726000-45741800	Weak transcription	Fetal Kidney	kidney
21	chr12:45726000-45743400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:45726600-45741600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:45726600-45741600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:45726600-45741800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:45726600-45747200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:45726800-45741800	Weak transcription	Fetal Lung	lung
27	chr12:45726800-45742000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:45726800-45743400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:45727400-45741800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:45728200-45741800	Weak transcription	Liver	Liver
31	chr12:45729800-45741400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:45731000-45742000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:45732400-45741800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr12:45732800-45741800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr12:45732800-45741800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:45732800-45741800	Weak transcription	Psoas Muscle	Psoas
37	chr12:45733000-45741800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:45733000-45742400	Weak transcription	K562	blood
39	chr12:45733000-45743400	Weak transcription	Ovary	ovary
40	chr12:45734000-45741600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:45734600-45747600	Weak transcription	Stomach Mucosa	stomach
42	chr12:45735400-45742400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:45735400-45755200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr12:45737400-45741600	Weak transcription	Hela-S3	cervix
45	chr12:45737400-45741800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr12:45737400-45741800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:45737400-45742000	Weak transcription	HUVEC	blood vessel
48	chr12:45737400-45742200	Weak transcription	NHLF	lung
49	chr12:45737400-45742600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:45737400-45748800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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