Variant report

Variant	rs6539176
Chromosome Location	chr12:105394749-105394750
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105379990..105383317-chr12:105392457..105395172,3	MCF-7	breast:
2	chr12:105394211..105395980-chr12:105415862..105418537,2	K562	blood:
3	chr12:105392063..105394759-chr12:105462525..105464694,2	K562	blood:

Variant related genes	Relation type
ENSG00000151131	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10778361	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10778363	0.96[ASN][1000 genomes]
rs10861298	0.85[CEU][hapmap]
rs10861299	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861301	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10861302	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10861303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10861304	0.97[ASN][1000 genomes]
rs10861308	0.96[ASN][1000 genomes]
rs10861309	0.96[ASN][1000 genomes]
rs10861310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10861311	0.96[ASN][1000 genomes]
rs10861313	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11112263	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11112284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112286	0.99[ASN][1000 genomes]
rs11112287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11112296	0.99[ASN][1000 genomes]
rs11112297	0.99[ASN][1000 genomes]
rs11112299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112306	0.98[ASN][1000 genomes]
rs1129593	0.95[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs12581510	0.96[ASN][1000 genomes]
rs12581542	0.94[ASN][1000 genomes]
rs16890	0.98[ASN][1000 genomes]
rs17036612	0.96[ASN][1000 genomes]
rs4281549	0.96[ASN][1000 genomes]
rs4318051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4331189	0.99[ASN][1000 genomes]
rs4473015	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964119	0.89[YRI][hapmap]
rs7134342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7297572	0.96[ASN][1000 genomes]
rs7302931	0.99[ASN][1000 genomes]
rs7304326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7308025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7308266	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7308568	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7308574	0.96[ASN][1000 genomes]
rs7309375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7311995	0.96[ASN][1000 genomes]
rs73387268	0.96[ASN][1000 genomes]
rs7958263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7970173	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869	chr12:105363425-105394904	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6539176	C12orf45	cis	Lymphoblastoid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105381800-105398000	Strong transcription	A549	lung
2	chr12:105381800-105407400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:105381800-105411400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:105382000-105397800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:105382000-105401400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:105382000-105401400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:105382200-105395000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:105382200-105395200	Strong transcription	Primary B cells from cord blood	blood
9	chr12:105382200-105395600	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr12:105382200-105401400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:105382200-105402000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:105382200-105402000	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:105382200-105402000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:105382200-105402600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:105382400-105401200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:105382400-105401400	Strong transcription	Liver	Liver
17	chr12:105382600-105397800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:105382800-105394800	Strong transcription	Primary T cells from cord blood	blood
19	chr12:105382800-105398000	Strong transcription	Adipose Nuclei	Adipose
20	chr12:105383000-105402000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:105383200-105396400	Strong transcription	Fetal Intestine Large	intestine
22	chr12:105383200-105398000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:105383400-105399000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr12:105383600-105394800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:105383600-105401600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:105383800-105397800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:105383800-105401200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:105384000-105395000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr12:105384000-105402000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:105384400-105394800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:105384800-105400000	Strong transcription	Brain Anterior Caudate	brain
32	chr12:105385200-105395000	Strong transcription	GM12878-XiMat	blood
33	chr12:105385800-105395200	Strong transcription	Fetal Kidney	kidney
34	chr12:105385800-105401400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:105385800-105408400	Weak transcription	Fetal Heart	heart
36	chr12:105387200-105396400	Weak transcription	Fetal Brain Male	brain
37	chr12:105387200-105397000	Weak transcription	Psoas Muscle	Psoas
38	chr12:105387200-105397200	Weak transcription	Small Intestine	intestine
39	chr12:105387400-105403000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr12:105387600-105395200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr12:105387600-105412200	Weak transcription	HepG2	liver
42	chr12:105389000-105430600	Weak transcription	Hela-S3	cervix
43	chr12:105389400-105406800	Weak transcription	NH-A	brain
44	chr12:105389400-105411200	Weak transcription	Osteobl	bone
45	chr12:105390200-105404000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:105390400-105395800	Weak transcription	Ovary	ovary
47	chr12:105390400-105397000	Weak transcription	HUVEC	blood vessel
48	chr12:105390600-105397000	Weak transcription	HSMMtube	muscle
49	chr12:105391000-105407400	Weak transcription	NHDF-Ad	bronchial
50	chr12:105391800-105398000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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