Variant report

Variant	rs11054941
Chromosome Location	chr12:12657195-12657196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12639514..12642208-chr12:12655232..12658211,2	MCF-7	breast:
2	chr12:12652584..12654636-chr12:12656031..12658126,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10743988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743989	0.82[AFR][1000 genomes]
rs10772570	0.81[ASN][1000 genomes]
rs10845552	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes]
rs10845559	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]
rs10845560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845563	0.81[CEU][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes]
rs10845567	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845572	0.83[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs11054937	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054940	0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs11054942	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]
rs11054947	0.91[ASN][1000 genomes]
rs11613385	0.95[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs12422540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1558822	0.95[ASN][1000 genomes]
rs2111271	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2287206	0.84[GIH][hapmap];0.80[MEX][hapmap]
rs2417190	1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs3815591	0.88[ASN][1000 genomes]
rs4255620	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763832	0.84[ASN][1000 genomes]
rs4763833	0.88[ASW][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs7137455	0.83[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs7294378	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7295305	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs7295427	0.86[ASN][1000 genomes]
rs7310652	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972902	0.88[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.95[ASN][1000 genomes]
rs933575	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs962927	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs962928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	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
3	nsv898811	chr12:12655443-12928295	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11054941	ETV6	cis	cerebellum	SCAN

Chromatin state (count:102 , 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	chr12:12630600-12661200	Weak transcription	NHEK	skin
3	chr12:12630800-12658200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:12630800-12658400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:12630800-12659600	Weak transcription	Esophagus	oesophagus
6	chr12:12630800-12681000	Weak transcription	Colonic Mucosa	Colon
7	chr12:12632800-12658200	Weak transcription	Ovary	ovary
8	chr12:12633000-12658600	Weak transcription	Fetal Kidney	kidney
9	chr12:12634400-12685200	Weak transcription	Hela-S3	cervix
10	chr12:12634800-12658800	Weak transcription	HSMMtube	muscle
11	chr12:12639400-12679600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:12639600-12659000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:12640000-12658000	Weak transcription	NHLF	lung
14	chr12:12640000-12658200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:12640000-12658200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:12640000-12658200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:12640400-12659200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:12641200-12658200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:12641600-12658800	Weak transcription	HUVEC	blood vessel
20	chr12:12641600-12663600	Weak transcription	Lung	lung
21	chr12:12641600-12686200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:12646200-12658200	Weak transcription	Aorta	Aorta
23	chr12:12646400-12658000	Weak transcription	K562	blood
24	chr12:12646800-12657400	Weak transcription	Left Ventricle	heart
25	chr12:12646800-12659200	Weak transcription	Gastric	stomach
26	chr12:12647000-12661400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:12647800-12658400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:12647800-12659200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr12:12649200-12658200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:12649200-12658200	Weak transcription	Pancreas	Pancrea
31	chr12:12649400-12658200	Weak transcription	Fetal Lung	lung
32	chr12:12649800-12658200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:12650000-12657200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:12650200-12658000	Weak transcription	Brain Anterior Caudate	brain
35	chr12:12650400-12658600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:12650800-12658000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:12652400-12659000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:12652600-12658600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr12:12652800-12665000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:12653000-12658200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:12653200-12658400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:12653400-12657800	Weak transcription	Adipose Nuclei	Adipose
43	chr12:12653400-12658000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr12:12653400-12658200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:12653400-12658400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:12653400-12659000	Enhancers	Brain Substantia Nigra	brain
47	chr12:12653600-12658000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:12653600-12658200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:12653600-12658200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr12:12653600-12658200	Weak transcription	Thymus	Thymus

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