Variant report

Variant	rs2249210
Chromosome Location	chr12:104342312-104342313
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104339816..104342339-chr12:104342509..104346802,3	MCF-7	breast:
2	chr12:104163154..104166859-chr12:104341815..104344175,3	K562	blood:
3	chr12:104327555..104329074-chr12:104341009..104342667,2	MCF-7	breast:
4	chr12:104342112..104344797-chr12:104358375..104361227,2	K562	blood:

Variant related genes	Relation type
ENSG00000204954	Chromatin interaction
ENSG00000139372	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs17034968	0.98[ASN][1000 genomes]
rs17034974	0.98[ASN][1000 genomes]
rs17035120	0.89[CHB][hapmap]
rs2293621	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2583259	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2722193	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2722195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3763995	0.94[CHB][hapmap];0.83[JPT][hapmap];0.97[ASN][1000 genomes]
rs3763996	0.98[ASN][1000 genomes]
rs4135042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4135067	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4135077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4964142	0.98[ASN][1000 genomes]
rs4964163	0.95[ASN][1000 genomes]
rs4964164	0.94[ASN][1000 genomes]
rs73177938	0.98[ASN][1000 genomes]
rs73177942	0.98[ASN][1000 genomes]
rs73177950	0.95[ASN][1000 genomes]
rs812498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2249210	C12orf73	cis	Artery Aorta	GTEx
rs2249210	C12orf73	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104325600-104348600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr12:104325600-104349800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:104325800-104348600	Strong transcription	Placenta	Placenta
4	chr12:104326000-104348800	Strong transcription	Fetal Muscle Leg	muscle
5	chr12:104326600-104348800	Strong transcription	Fetal Muscle Trunk	muscle
6	chr12:104326800-104344800	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr12:104326800-104348800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:104326800-104348800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:104327000-104348200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:104327000-104348600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:104327200-104345000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:104327200-104345400	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr12:104327200-104348000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:104327200-104348200	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:104327200-104348400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr12:104327200-104348600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr12:104327200-104348600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:104327200-104348600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:104327200-104348600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:104327200-104348600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:104327200-104348800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:104327200-104348800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:104327200-104349000	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:104327200-104349200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:104327400-104348000	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr12:104327400-104348000	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:104327400-104348200	Strong transcription	HSMM	muscle
28	chr12:104327800-104348400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:104327800-104348400	Strong transcription	Primary B cells from cord blood	blood
30	chr12:104328200-104344800	Strong transcription	Brain Substantia Nigra	brain
31	chr12:104328200-104348600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:104328200-104348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:104328400-104345400	Strong transcription	Hela-S3	cervix
34	chr12:104328400-104347000	Strong transcription	Fetal Brain Female	brain
35	chr12:104328400-104348200	Strong transcription	NHDF-Ad	bronchial
36	chr12:104328400-104348600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:104328400-104348600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:104328400-104348600	Strong transcription	Osteobl	bone
39	chr12:104328400-104349000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:104329000-104348600	Strong transcription	Fetal Intestine Large	intestine
41	chr12:104329200-104348400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:104329200-104348800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr12:104329400-104349000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:104329600-104347600	Strong transcription	NH-A	brain
45	chr12:104329600-104348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:104329600-104348400	Strong transcription	Primary B cells from peripheral blood	blood
47	chr12:104329600-104348800	Strong transcription	HUVEC	blood vessel
48	chr12:104329600-104349200	Strong transcription	Fetal Lung	lung
49	chr12:104329800-104343400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:104329800-104344800	Strong transcription	Rectal Smooth Muscle	rectum

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