Variant report

Variant	rs12405904
Chromosome Location	chr1:225651167-225651168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225649550..225651644-chr1:225657315..225659303,2	MCF-7	breast:
2	chr1:225646305..225648757-chr1:225649524..225652760,3	K562	blood:
3	chr1:225615091..225616977-chr1:225649695..225651542,2	MCF-7	breast:
4	chr1:225597465..225599804-chr1:225650818..225652643,4	K562	blood:
5	chr1:225597626..225599804-chr1:225650818..225652643,2	K562	blood:

Variant related genes	Relation type
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10915829	0.84[ASN][1000 genomes]
rs12026034	0.84[ASN][1000 genomes]
rs12239415	0.83[ASN][1000 genomes]
rs12405879	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340871	0.84[ASN][1000 genomes]
rs1340872	0.84[ASN][1000 genomes]
rs28620013	0.84[ASN][1000 genomes]
rs3795443	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs55751087	0.81[ASN][1000 genomes]
rs58269599	0.84[ASN][1000 genomes]
rs59912270	0.84[ASN][1000 genomes]
rs6681559	0.84[ASN][1000 genomes]
rs6684314	0.84[ASN][1000 genomes]
rs6684956	0.83[ASN][1000 genomes]
rs6694938	0.81[ASN][1000 genomes]
rs74146931	0.83[ASN][1000 genomes]
rs74146994	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12405904	RP11-496N12.9	cis	Skin Sun Exposed Lower leg	GTEx
rs12405904	LBR	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225642400-225653000	Weak transcription	Primary B cells from cord blood	blood
2	chr1:225642400-225655200	Weak transcription	Small Intestine	intestine
3	chr1:225642600-225655000	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:225642800-225652800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:225646400-225653600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:225647000-225651600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr1:225647000-225651600	Enhancers	Fetal Muscle Leg	muscle
8	chr1:225647000-225653600	Enhancers	Esophagus	oesophagus
9	chr1:225647000-225654600	Enhancers	Fetal Thymus	thymus
10	chr1:225647000-225654800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:225647200-225651600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:225647400-225651200	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr1:225647400-225654800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:225647600-225652000	Enhancers	Fetal Stomach	stomach
15	chr1:225647600-225653800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:225647800-225653400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:225648000-225651400	Enhancers	Fetal Brain Male	brain
18	chr1:225648000-225652600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:225648400-225653400	Weak transcription	Fetal Intestine Large	intestine
20	chr1:225648600-225651200	Enhancers	Fetal Brain Female	brain
21	chr1:225648600-225652800	Weak transcription	Fetal Kidney	kidney
22	chr1:225648800-225651400	Enhancers	Ovary	ovary
23	chr1:225648800-225652000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr1:225648800-225652200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:225648800-225652600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:225648800-225652600	Weak transcription	Osteobl	bone
27	chr1:225648800-225654600	Weak transcription	HUVEC	blood vessel
28	chr1:225649000-225652600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:225649000-225653200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:225649000-225654600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:225649200-225652000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr1:225649200-225652400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:225649200-225652800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:225649200-225654400	Weak transcription	Primary T cells from cord blood	blood
35	chr1:225649400-225653400	Weak transcription	Dnd41	blood
36	chr1:225649600-225651200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:225649600-225652600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:225649800-225651200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:225649800-225654800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:225649800-225662600	Weak transcription	Pancreas	Pancrea
41	chr1:225650000-225651200	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr1:225650000-225651200	Enhancers	Fetal Lung	lung
43	chr1:225650000-225651400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:225650000-225651800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr1:225650000-225652600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:225650000-225653200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:225650000-225653600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:225650200-225651600	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr1:225650200-225651600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr1:225650200-225652000	Enhancers	Rectal Smooth Muscle	rectum

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