Variant report

Variant	rs28647680
Chromosome Location	chr12:124008459-124008460
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123991512..123994441-chr12:124007477..124009377,2	MCF-7	breast:
2	chr12:124004156..124006124-chr12:124006338..124008764,2	MCF-7	breast:
3	chr12:124007811..124010230-chr12:124011879..124014265,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1050443	1.00[JPT][hapmap]
rs1050448	1.00[JPT][hapmap]
rs11057297	0.89[CEU][hapmap]
rs11612927	1.00[JPT][hapmap]
rs12809853	1.00[JPT][hapmap]
rs13302918	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13303334	0.84[YRI][hapmap]
rs15587	1.00[JPT][hapmap]
rs28492040	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28604461	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28833471	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204541	1.00[JPT][hapmap]
rs34351395	0.95[YRI][hapmap]
rs34734800	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34944476	0.81[EUR][1000 genomes]
rs4930704	0.83[ASN][1000 genomes]
rs4930717	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930737	1.00[JPT][hapmap]
rs61953540	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61953541	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488877	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6488878	0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7313751	0.83[ASN][1000 genomes]
rs7398935	0.83[ASN][1000 genomes]
rs7956299	0.83[ASN][1000 genomes]
rs7962151	0.83[ASN][1000 genomes]
rs7963804	0.83[ASN][1000 genomes]
rs7974279	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28647680	TCTN2	cis	parietal	SCAN
rs28647680	PRKAB1	cis	parietal	SCAN
rs28647680	PERP	trans	lymphoblastoid	seeQTL
rs28647680	TCTN2	cis	cerebellum	SCAN
rs28647680	ANAPC5	cis	parietal	SCAN
rs28647680	MPHOSPH9	cis	cerebellum	SCAN
rs28647680	GPR81	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123944600-124012200	Strong transcription	Fetal Stomach	stomach
2	chr12:123970000-124016400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr12:123992600-124012800	Weak transcription	Thymus	Thymus
4	chr12:123993600-124011200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:123994400-124016200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:123994600-124016200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:123995200-124016400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:123995400-124009400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:123999200-124015800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr12:123999400-124016400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:124000200-124012400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:124000600-124009200	Strong transcription	Liver	Liver
13	chr12:124000600-124009200	Strong transcription	Fetal Brain Female	brain
14	chr12:124000600-124009200	Strong transcription	Ovary	ovary
15	chr12:124000600-124009200	Strong transcription	Spleen	Spleen
16	chr12:124000600-124009400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:124000600-124009400	Strong transcription	Adipose Nuclei	Adipose
18	chr12:124000600-124009600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:124000600-124009800	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:124000600-124011400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:124000600-124015000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr12:124000800-124009000	Strong transcription	Brain Germinal Matrix	brain
23	chr12:124001000-124009000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:124001000-124016400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:124001200-124009000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:124001200-124017400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:124001400-124017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:124002000-124016800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr12:124003000-124015400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr12:124004000-124009200	Strong transcription	Fetal Intestine Large	intestine
31	chr12:124004000-124009200	Strong transcription	Lung	lung
32	chr12:124004200-124009200	Strong transcription	Fetal Lung	lung
33	chr12:124004400-124008800	Strong transcription	Fetal Intestine Small	intestine
34	chr12:124004600-124009000	Strong transcription	Brain Substantia Nigra	brain
35	chr12:124004600-124009200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:124004600-124009200	Strong transcription	Brain Cingulate Gyrus	brain
37	chr12:124004600-124009200	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr12:124004600-124011200	Weak transcription	Psoas Muscle	Psoas
39	chr12:124004600-124016800	Weak transcription	Stomach Mucosa	stomach
40	chr12:124004800-124008600	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr12:124004800-124008600	Strong transcription	Aorta	Aorta
42	chr12:124004800-124009200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:124004800-124009200	Strong transcription	Brain Angular Gyrus	brain
44	chr12:124004800-124009200	Strong transcription	Osteobl	bone
45	chr12:124004800-124009400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:124004800-124009400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:124004800-124009400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:124004800-124009400	Strong transcription	Brain Anterior Caudate	brain
49	chr12:124004800-124009400	Strong transcription	Colon Smooth Muscle	Colon
50	chr12:124004800-124009400	Strong transcription	A549	lung

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