Variant report

Variant	rs11043285
Chromosome Location	chr12:122443534-122443535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122442757..122445214-chr12:122447677..122450605,3	K562	blood:
2	chr12:122439495..122442449-chr12:122442694..122444959,2	MCF-7	breast:
3	chr12:122440790..122443569-chr12:122445704..122448468,2	MCF-7	breast:
4	chr12:122237113..122238694-chr12:122441857..122444463,2	K562	blood:
5	chr12:122441336..122445469-chr12:122458589..122461636,5	MCF-7	breast:
6	chr12:122439280..122442623-chr12:122442639..122445815,4	K562	blood:

Variant related genes	Relation type
ENSG00000158023	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000110987	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10431199	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840642	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11043216	1.00[JPT][hapmap]
rs11043229	0.81[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11043237	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11043242	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11043255	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11043263	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11043276	1.00[MEX][hapmap]
rs11043277	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11043286	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043290	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043292	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11043295	0.94[ASN][1000 genomes]
rs11829607	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12230823	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1610041	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2707058	0.87[CHD][hapmap];1.00[TSI][hapmap]
rs34768683	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3847694	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs4069668	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56040016	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56122558	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56142842	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58326739	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59922210	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7137708	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs7138296	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7139277	1.00[MEX][hapmap]
rs7313252	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs73415674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73415687	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73415696	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7958406	1.00[JPT][hapmap]
rs7961660	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971538	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978386	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11043285	SH3BP1	trans	brain	seeQTL
rs11043285	LAMB3	trans	brain	seeQTL
rs11043285	HS3ST2	trans	brain	seeQTL

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122438000-122444400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:122438600-122443600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr12:122439800-122445200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:122440400-122445800	Enhancers	Primary hematopoietic stem cells	blood
5	chr12:122440800-122445000	Weak transcription	Brain Germinal Matrix	brain
6	chr12:122441000-122445600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:122441600-122443600	Enhancers	Spleen	Spleen
8	chr12:122441600-122443600	Flanking Active TSS	Dnd41	blood
9	chr12:122441600-122444000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr12:122441600-122444200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr12:122441600-122444800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr12:122441600-122444800	Flanking Active TSS	Fetal Thymus	thymus
13	chr12:122441600-122445800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr12:122441800-122443600	Flanking Active TSS	Thymus	Thymus
15	chr12:122441800-122444200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr12:122441800-122444200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:122441800-122444200	Enhancers	GM12878-XiMat	blood
18	chr12:122441800-122444400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr12:122441800-122444400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr12:122441800-122445800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:122441800-122445800	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr12:122442000-122443600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:122442000-122444400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:122442000-122444400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:122442000-122446800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:122442200-122444200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:122442200-122444200	Enhancers	Fetal Muscle Trunk	muscle
28	chr12:122442200-122445000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr12:122442400-122443600	Enhancers	HSMMtube	muscle
30	chr12:122442600-122458800	Weak transcription	Aorta	Aorta
31	chr12:122442800-122445600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:122443000-122443800	Enhancers	Primary T cells from cord blood	blood
33	chr12:122443000-122444400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:122443000-122444400	Weak transcription	Fetal Brain Male	brain
35	chr12:122443000-122445000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:122443000-122445600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:122443000-122446000	Weak transcription	Adipose Nuclei	Adipose
38	chr12:122443000-122449000	Enhancers	Primary B cells from peripheral blood	blood
39	chr12:122443000-122458800	Weak transcription	Brain Anterior Caudate	brain
40	chr12:122443200-122443600	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr12:122443400-122443600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:122443400-122444400	Weak transcription	Fetal Heart	heart
43	chr12:122443400-122444400	Weak transcription	Left Ventricle	heart
44	chr12:122443400-122444400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:122443400-122446200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:122443400-122446600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr12:122443400-122446800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:122443400-122446800	Weak transcription	NHEK	skin
49	chr12:122443400-122458800	Weak transcription	Right Ventricle	heart
50	chr12:122443400-122459000	Weak transcription	Right Atrium	heart

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