Variant report

Variant	rs2576975
Chromosome Location	chr12:104348430-104348431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104348297..104351124-chr12:104530392..104533056,3	MCF-7	breast:
2	chr12:104234122..104238773-chr12:104347839..104352988,5	MCF-7	breast:
3	chr12:104348328..104351209-chr12:104680724..104683661,2	K562	blood:
4	chr12:104347143..104348904-chr12:104363665..104366015,2	K562	blood:
5	chr12:104320418..104331406-chr12:104346801..104355501,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166598	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000265072	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10861149	0.97[ASN][1000 genomes]
rs11111852	0.94[ASN][1000 genomes]
rs11111854	1.00[ASN][1000 genomes]
rs1165692	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165694	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165695	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165696	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1177457	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179177	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227567	0.97[ASN][1000 genomes]
rs15805	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293617	0.96[ASN][1000 genomes]
rs2293618	0.96[ASN][1000 genomes]
rs2583254	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2583262	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583264	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700508	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700509	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722190	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722191	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2722192	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964375	0.94[ASN][1000 genomes]
rs703657	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7645	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2576975	C12orf73	cis	Thyroid	GTEx
rs2576975	C12orf73	cis	Artery Aorta	GTEx
rs2576975	KRTHB5	Cis_1M	lymphoblastoid	RTeQTL
rs2576975	C12orf73	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 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	chr12:104326800-104348800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:104326800-104348800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:104327000-104348600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:104327200-104348600	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr12:104327200-104348600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:104327200-104348600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:104327200-104348600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr12:104327200-104348600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:104327200-104348800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:104327200-104348800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:104327200-104349000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:104327200-104349200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:104328200-104348600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:104328200-104348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:104328400-104348600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:104328400-104348600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:104328400-104348600	Strong transcription	Osteobl	bone
23	chr12:104328400-104349000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:104329000-104348600	Strong transcription	Fetal Intestine Large	intestine
25	chr12:104329200-104348800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr12:104329400-104349000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:104329600-104348800	Strong transcription	HUVEC	blood vessel
28	chr12:104329600-104349200	Strong transcription	Fetal Lung	lung
29	chr12:104329800-104349000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:104330200-104348600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:104330200-104348600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:104330200-104348600	Strong transcription	Brain Anterior Caudate	brain
33	chr12:104330200-104348600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:104330200-104348600	Strong transcription	HMEC	breast
35	chr12:104330200-104348800	Strong transcription	Fetal Thymus	thymus
36	chr12:104330200-104349000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:104330800-104348600	Strong transcription	Liver	Liver
38	chr12:104330800-104348600	Strong transcription	Duodenum Mucosa	Duodenum
39	chr12:104332200-104348600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:104332200-104348800	Strong transcription	Primary T cells from cord blood	blood
41	chr12:104334000-104349600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr12:104334800-104348600	Strong transcription	HSMMtube	muscle
43	chr12:104335000-104348600	Strong transcription	Ovary	ovary
44	chr12:104336200-104348800	Strong transcription	A549	lung
45	chr12:104337000-104350000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:104341200-104349400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr12:104341600-104349200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:104343000-104348600	Strong transcription	Fetal Kidney	kidney
49	chr12:104344400-104349600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:104344800-104349000	Weak transcription	Small Intestine	intestine

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