Variant report

Variant	rs6487933
Chromosome Location	chr12:30875969-30875970
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:30874193..30876323-chr12:30878456..30880055,2	MCF-7	breast:
2	chr12:30873989..30876161-chr12:30882360..30885306,2	K562	blood:

Variant related genes	Relation type
ENSG00000110888	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10743733	0.81[AMR][1000 genomes]
rs10743734	0.81[AMR][1000 genomes]
rs10771754	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10771764	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10771765	0.87[ASN][1000 genomes]
rs10771766	0.87[ASN][1000 genomes]
rs10771767	0.87[ASN][1000 genomes]
rs10771768	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10771769	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10843822	0.85[CHB][hapmap]
rs10843824	0.86[CHB][hapmap]
rs10843833	0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs10843835	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11051013	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11051052	0.92[CEU][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11051053	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11051061	0.81[CHB][hapmap]
rs12303852	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs12305697	0.87[ASN][1000 genomes]
rs12370429	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13656	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1371049	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1371053	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1866416	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2099661	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2289301	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2304630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2352210	0.87[EUR][1000 genomes]
rs2352217	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs33132	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35925509	0.86[ASN][1000 genomes]
rs3782685	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4082413	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4143103	0.87[EUR][1000 genomes]
rs4930935	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4930936	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4931356	0.86[EUR][1000 genomes]
rs6487932	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6487938	0.84[ASN][1000 genomes]
rs6487939	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs7136079	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs718368	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7298007	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7298180	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7304221	0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7304879	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7304976	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7311651	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs794152	0.85[CEU][hapmap]
rs7952744	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs7957141	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7957226	0.87[ASN][1000 genomes]
rs7963494	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7968587	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7971762	0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7971870	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9300199	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][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	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6487933	IPO8	cis	multi-tissue	Pritchard
rs6487933	IPO8	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30849200-30881600	Weak transcription	Right Ventricle	heart
2	chr12:30849600-30881200	Weak transcription	Psoas Muscle	Psoas
3	chr12:30849600-30881600	Weak transcription	Aorta	Aorta
4	chr12:30857400-30881800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:30858000-30891800	Weak transcription	Fetal Heart	heart
6	chr12:30859200-30892200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:30859400-30883400	Weak transcription	Colonic Mucosa	Colon
8	chr12:30859800-30877000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:30860400-30881600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:30861000-30879000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:30861400-30881600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:30861400-30885000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:30861400-30906200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:30861400-30906600	Weak transcription	Small Intestine	intestine
15	chr12:30861800-30877800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:30861800-30879000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr12:30861800-30884600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:30861800-30894600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:30861800-30895200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:30862000-30877800	Strong transcription	HMEC	breast
21	chr12:30862000-30878800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:30862000-30879000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:30862200-30879000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:30862200-30895000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:30862400-30876600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:30862400-30895600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:30863400-30877200	Weak transcription	Pancreas	Pancrea
28	chr12:30863400-30877600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:30863400-30881600	Weak transcription	Gastric	stomach
30	chr12:30863400-30882800	Weak transcription	Brain Substantia Nigra	brain
31	chr12:30863400-30885200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:30863400-30891000	Weak transcription	GM12878-XiMat	blood
33	chr12:30863400-30906400	Weak transcription	Spleen	Spleen
34	chr12:30863400-30906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:30864600-30905200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr12:30865000-30881600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr12:30865400-30881600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:30867200-30881600	Weak transcription	Lung	lung
39	chr12:30867400-30877400	Strong transcription	HUVEC	blood vessel
40	chr12:30867400-30881600	Weak transcription	Esophagus	oesophagus
41	chr12:30867400-30884400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:30868600-30876800	Weak transcription	Ovary	ovary
43	chr12:30868800-30878200	Strong transcription	NHEK	skin
44	chr12:30869400-30876000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:30869600-30877400	Weak transcription	Fetal Thymus	thymus
46	chr12:30869600-30881600	Weak transcription	Brain Angular Gyrus	brain
47	chr12:30869600-30886000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:30869800-30889000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr12:30870000-30876200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:30870000-30876600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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