Variant report

Variant	rs10845559
Chromosome Location	chr12:12646478-12646479
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12643142..12644757-chr12:12645381..12648713,3	MCF-7	breast:
2	chr12:12644427..12647332-chr12:12650507..12652988,2	K562	blood:
3	chr12:12645901..12648123-chr12:12648969..12651125,3	MCF-7	breast:
4	chr12:12641664..12643541-chr12:12644631..12646800,2	K562	blood:
5	chr12:12645183..12647034-chr12:12654341..12656540,2	MCF-7	breast:
6	chr12:12626427..12628119-chr12:12644483..12647018,2	K562	blood:
7	chr12:12634008..12636431-chr12:12645657..12647328,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10743988	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772570	0.82[ASN][1000 genomes]
rs10845552	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes]
rs10845560	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845563	0.81[CEU][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap]
rs10845567	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845572	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs11054937	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054940	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs11054941	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054942	0.83[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs11054947	0.90[ASN][1000 genomes]
rs11613385	0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs12422540	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1558822	0.93[ASN][1000 genomes]
rs2111271	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2287206	0.86[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs2417190	0.90[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs3815591	0.88[ASN][1000 genomes]
rs4255620	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763832	0.84[ASN][1000 genomes]
rs4763833	0.83[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs7137455	0.90[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs7294378	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7295305	0.90[CHB][hapmap];0.92[CHD][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs7295427	0.86[ASN][1000 genomes]
rs7310652	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972902	0.83[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.93[ASN][1000 genomes]
rs933575	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs962927	0.92[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs962928	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic 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	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10845559	ETV6	cis	cerebellum	SCAN
rs10845559	LOH12CR1	cis	lymphoblastoid	seeQTL
rs10845559	LOH12CR1	cis	multi-tissue	Pritchard

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12610800-12658000	Weak transcription	NHDF-Ad	bronchial
2	chr12:12622600-12653800	Weak transcription	Fetal Heart	heart
3	chr12:12626800-12653600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:12628600-12647600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:12628800-12655800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:12630600-12661200	Weak transcription	NHEK	skin
7	chr12:12630800-12655800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:12630800-12658200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:12630800-12658400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:12630800-12659600	Weak transcription	Esophagus	oesophagus
11	chr12:12630800-12681000	Weak transcription	Colonic Mucosa	Colon
12	chr12:12632800-12658200	Weak transcription	Ovary	ovary
13	chr12:12633000-12658600	Weak transcription	Fetal Kidney	kidney
14	chr12:12633400-12648800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:12634400-12685200	Weak transcription	Hela-S3	cervix
16	chr12:12634800-12658800	Weak transcription	HSMMtube	muscle
17	chr12:12635000-12647400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:12636000-12653400	Weak transcription	Right Ventricle	heart
19	chr12:12636200-12655800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:12636800-12647400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:12636800-12656800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:12637200-12651600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:12639000-12646600	Genic enhancers	Fetal Intestine Small	intestine
24	chr12:12639200-12647000	Genic enhancers	HepG2	liver
25	chr12:12639400-12648800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:12639400-12652800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:12639400-12679600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:12639600-12648000	Weak transcription	Fetal Brain Female	brain
29	chr12:12639600-12655800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr12:12639600-12659000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:12639800-12647200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:12640000-12646600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:12640000-12648800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:12640000-12648800	Weak transcription	Fetal Lung	lung
35	chr12:12640000-12652800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:12640000-12656600	Weak transcription	Colon Smooth Muscle	Colon
37	chr12:12640000-12658000	Weak transcription	NHLF	lung
38	chr12:12640000-12658200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:12640000-12658200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:12640000-12658200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:12640200-12647000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:12640200-12647400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:12640200-12649200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:12640200-12649600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr12:12640200-12652200	Weak transcription	Placenta	Placenta
46	chr12:12640200-12652800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:12640200-12656600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:12640400-12659200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:12640600-12649000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:12641200-12658200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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