Variant report

Variant	rs2440715
Chromosome Location	chr12:105614408-105614409
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105604459..105610765-chr12:105612400..105619000,9	MCF-7	breast:
2	chr12:105608691..105610894-chr12:105612066..105614500,4	MCF-7	breast:
3	chr12:105610784..105617210-chr12:105628529..105631630,8	MCF-7	breast:
4	chr12:105606795..105619301-chr12:105624368..105633184,26	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136044	Chromatin interaction
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10746010	1.00[ASN][1000 genomes]
rs10778367	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs10778368	1.00[ASN][1000 genomes]
rs10861347	1.00[CHB][hapmap]
rs10861371	1.00[CHB][hapmap]
rs10861400	1.00[CHB][hapmap]
rs10861407	1.00[CHB][hapmap]
rs10861409	1.00[CHB][hapmap]
rs11112434	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11112467	1.00[ASN][1000 genomes]
rs11112475	1.00[CHB][hapmap]
rs1196742	1.00[ASN][1000 genomes]
rs1196745	1.00[ASN][1000 genomes]
rs1196748	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196749	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196753	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196754	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196756	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196759	1.00[ASN][1000 genomes]
rs1196760	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196765	1.00[ASN][1000 genomes]
rs1196777	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1196793	1.00[CHB][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs1196795	0.85[MEX][hapmap]
rs1196797	0.85[MEX][hapmap]
rs1196800	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196801	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196805	1.00[ASN][1000 genomes]
rs1196806	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1196807	1.00[ASN][1000 genomes]
rs1196808	1.00[ASN][1000 genomes]
rs1196811	0.81[CEU][hapmap]
rs1196813	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196817	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196818	1.00[CHB][hapmap]
rs1196819	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1196820	1.00[ASN][1000 genomes]
rs1196823	1.00[ASN][1000 genomes]
rs1196825	1.00[ASN][1000 genomes]
rs1196831	1.00[ASN][1000 genomes]
rs1196833	1.00[ASN][1000 genomes]
rs1196839	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196841	1.00[ASN][1000 genomes]
rs1196842	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1196844	1.00[ASN][1000 genomes]
rs1196848	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196851	0.83[CEU][hapmap]
rs1196852	1.00[CHB][hapmap]
rs1196853	1.00[ASN][1000 genomes]
rs1196857	1.00[ASN][1000 genomes]
rs1196859	1.00[ASN][1000 genomes]
rs1196861	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1196862	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1196864	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1196869	0.83[CEU][hapmap];1.00[MEX][hapmap]
rs1196871	1.00[ASN][1000 genomes]
rs1196872	1.00[MEX][hapmap]
rs1196873	0.83[CEU][hapmap];1.00[MEX][hapmap]
rs1196874	1.00[ASN][1000 genomes]
rs1196881	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196884	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs1206559	1.00[ASN][1000 genomes]
rs1209308	1.00[ASN][1000 genomes]
rs1209637	0.85[MEX][hapmap]
rs1211276	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1211277	1.00[ASN][1000 genomes]
rs12822081	1.00[CHB][hapmap]
rs1621553	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1663564	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1663565	1.00[ASN][1000 genomes]
rs1732370	1.00[ASN][1000 genomes]
rs2166142	1.00[ASN][1000 genomes]
rs2257156	0.83[CEU][hapmap];1.00[MEX][hapmap]
rs2374449	0.83[CEU][hapmap]
rs2440718	1.00[ASN][1000 genomes]
rs2464173	1.00[ASN][1000 genomes]
rs2464175	0.83[CEU][hapmap]
rs2464181	1.00[ASN][1000 genomes]
rs2888846	1.00[CHB][hapmap]
rs4356312	1.00[ASN][1000 genomes]
rs4356313	1.00[ASN][1000 genomes]
rs4372534	1.00[ASN][1000 genomes]
rs4390426	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4545651	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4964122	1.00[ASN][1000 genomes]
rs4964331	0.83[CEU][hapmap]
rs6539183	1.00[ASW][hapmap];0.83[CEU][hapmap];0.82[MEX][hapmap]
rs6539187	1.00[ASN][1000 genomes]
rs7132040	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs7132855	0.91[CEU][hapmap]
rs7299225	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7302174	1.00[CHB][hapmap]
rs7959385	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7963877	1.00[ASW][hapmap];0.83[CEU][hapmap];0.82[MEX][hapmap]
rs935240	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs935241	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs935242	1.00[ASN][1000 genomes]
rs935244	1.00[CHB][hapmap];0.85[MEX][hapmap]
rs935246	1.00[ASN][1000 genomes]
rs9645791	1.00[CHB][hapmap]

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	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers 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	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2440715	ALDH1L2	cis	cerebellum	SCAN
rs2440715	APPL2	cis	cerebellum	SCAN
rs2440715	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:105571400-105617800	Weak transcription	K562	blood
4	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:105590200-105620000	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:105590400-105618800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr12:105591000-105619400	Strong transcription	Primary T cells from cord blood	blood
11	chr12:105595000-105618800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr12:105595800-105616600	Strong transcription	Primary hematopoietic stem cells	blood
13	chr12:105596000-105617000	Strong transcription	Fetal Lung	lung
14	chr12:105596400-105621800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:105600800-105626800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:105601000-105615800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:105601000-105619200	Weak transcription	GM12878-XiMat	blood
18	chr12:105601400-105615800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:105604200-105616200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:105604400-105618400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:105605600-105628400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:105606400-105614800	Strong transcription	Primary B cells from cord blood	blood
23	chr12:105606600-105616600	Strong transcription	Fetal Thymus	thymus
24	chr12:105606800-105617000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr12:105607200-105615800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:105607200-105618600	Genic enhancers	Fetal Intestine Large	intestine
27	chr12:105608200-105615600	Strong transcription	Fetal Brain Female	brain
28	chr12:105608600-105618200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr12:105609000-105618600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:105609200-105615200	Weak transcription	HMEC	breast
31	chr12:105609200-105620400	Genic enhancers	Fetal Intestine Small	intestine
32	chr12:105609200-105622400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:105609200-105626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:105609200-105628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:105609400-105615200	Weak transcription	HepG2	liver
36	chr12:105609400-105618600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:105609400-105619400	Strong transcription	Osteobl	bone
38	chr12:105610200-105618800	Strong transcription	Thymus	Thymus
39	chr12:105610600-105616000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:105610800-105615800	Weak transcription	Esophagus	oesophagus
41	chr12:105610800-105620000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:105611000-105620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:105611000-105620200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:105611200-105620200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:105611200-105621200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr12:105611200-105628200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:105611400-105614600	Weak transcription	A549	lung
48	chr12:105611400-105615000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr12:105611400-105615400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:105611400-105619600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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