Variant report

Variant	rs12422540
Chromosome Location	chr12:12645696-12645697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12641707..12643541-chr12:12643903..12646131,2	K562	blood:
2	chr12:12643142..12644757-chr12:12645381..12648713,3	MCF-7	breast:
3	chr12:12644427..12647332-chr12:12650507..12652988,2	K562	blood:
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: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10743988	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772570	0.82[ASN][1000 genomes]
rs10845552	0.87[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes]
rs10845559	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]
rs10845560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845567	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845572	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs11054937	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054940	0.95[CHB][hapmap];0.80[JPT][hapmap];0.93[ASN][1000 genomes]
rs11054941	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]
rs11054942	1.00[CHB][hapmap];0.80[JPT][hapmap];0.93[ASN][1000 genomes]
rs11054947	0.90[ASN][1000 genomes]
rs11613385	0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs1558822	0.93[ASN][1000 genomes]
rs2111271	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2417190	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs3815591	0.88[ASN][1000 genomes]
rs4255620	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763832	0.84[ASN][1000 genomes]
rs4763833	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs7137455	1.00[CHB][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs7294378	0.91[ASN][1000 genomes]
rs7295305	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs7295427	0.86[ASN][1000 genomes]
rs7310652	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972902	0.95[CHB][hapmap];0.93[ASN][1000 genomes]
rs933575	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs962927	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs962928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[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

No data

Chromatin state (count:109 , 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	chr12:12621600-12646000	Weak transcription	Psoas Muscle	Psoas
3	chr12:12621600-12646200	Weak transcription	Brain Germinal Matrix	brain
4	chr12:12622600-12653800	Weak transcription	Fetal Heart	heart
5	chr12:12626800-12653600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:12627800-12646200	Weak transcription	Fetal Brain Male	brain
7	chr12:12628600-12647600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:12628800-12655800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:12630600-12661200	Weak transcription	NHEK	skin
10	chr12:12630800-12655800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:12630800-12658200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:12630800-12658400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:12630800-12659600	Weak transcription	Esophagus	oesophagus
14	chr12:12630800-12681000	Weak transcription	Colonic Mucosa	Colon
15	chr12:12632800-12658200	Weak transcription	Ovary	ovary
16	chr12:12633000-12658600	Weak transcription	Fetal Kidney	kidney
17	chr12:12633400-12648800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:12634400-12685200	Weak transcription	Hela-S3	cervix
19	chr12:12634800-12658800	Weak transcription	HSMMtube	muscle
20	chr12:12635000-12647400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:12636000-12653400	Weak transcription	Right Ventricle	heart
22	chr12:12636200-12655800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:12636600-12646200	Weak transcription	Primary B cells from cord blood	blood
24	chr12:12636800-12647400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:12636800-12656800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:12637200-12651600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:12639000-12646600	Genic enhancers	Fetal Intestine Small	intestine
28	chr12:12639200-12647000	Genic enhancers	HepG2	liver
29	chr12:12639400-12648800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:12639400-12652800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:12639400-12679600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:12639600-12648000	Weak transcription	Fetal Brain Female	brain
33	chr12:12639600-12655800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:12639600-12659000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:12639800-12647200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:12640000-12646600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:12640000-12648800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:12640000-12648800	Weak transcription	Fetal Lung	lung
39	chr12:12640000-12652800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:12640000-12656600	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:12640000-12658000	Weak transcription	NHLF	lung
42	chr12:12640000-12658200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:12640000-12658200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:12640000-12658200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:12640200-12645800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:12640200-12646000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:12640200-12646000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:12640200-12647000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:12640200-12647400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr12:12640200-12649200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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