Variant report

Variant	rs2365439
Chromosome Location	chr11:72431231-72431232
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:72430803..72433012-chr11:72434377..72436437,3	MCF-7	breast:
2	chr11:72422011..72424823-chr11:72430319..72431907,2	MCF-7	breast:
3	chr11:72429291..72431347-chr11:72435489..72438206,2	K562	blood:
4	chr11:72430307..72432258-chr11:72433856..72435880,2	MCF-7	breast:
5	chr11:72427542..72429481-chr11:72430563..72432228,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186635	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10793039	0.84[CHD][hapmap]
rs10793040	0.87[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs10898866	0.83[GIH][hapmap]
rs1681503	0.84[ASN][1000 genomes]
rs624030	0.90[ASN][1000 genomes]
rs660043	0.87[CHB][hapmap]
rs7110801	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7125221	0.82[TSI][hapmap]
rs745995	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs900611	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1806140	chr11:72268466-72546175	Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
2	nsv832207	chr11:72272750-72469122	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
3	esv3394774	chr11:72320884-72694077	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv555408	chr11:72405223-72441431	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv468636	chr11:72405868-72431679	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv555410	chr11:72405868-72431679	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2365439	STARD10	cis	Whole Blood	GTEx
rs2365439	STARD10	cis	cerebellum	SCAN
rs2365439	PDE2A	cis	parietal	SCAN
rs2365439	ARAP1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72409000-72432600	Strong transcription	HepG2	liver
2	chr11:72418000-72434800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr11:72418000-72441000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr11:72418800-72432000	Weak transcription	A549	lung
5	chr11:72419000-72433200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:72419400-72431800	Weak transcription	Fetal Kidney	kidney
7	chr11:72422400-72433200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:72423200-72432200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:72424000-72431400	Weak transcription	NH-A	brain
10	chr11:72424200-72431600	Weak transcription	NHDF-Ad	bronchial
11	chr11:72424200-72433000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:72424600-72431800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:72424600-72441200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr11:72425400-72431800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:72426000-72431800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr11:72426400-72432800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr11:72427800-72431400	Genic enhancers	Spleen	Spleen
18	chr11:72428200-72432400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr11:72428200-72432800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:72428400-72431600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:72428600-72431400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:72428800-72431400	Enhancers	Stomach Mucosa	stomach
23	chr11:72428800-72431800	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr11:72428800-72432000	Weak transcription	Aorta	Aorta
25	chr11:72429200-72431400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:72429200-72431400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:72429200-72432800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:72429400-72431400	Enhancers	Ovary	ovary
29	chr11:72429400-72431600	Enhancers	Brain Germinal Matrix	brain
30	chr11:72429400-72431600	Enhancers	Pancreas	Pancrea
31	chr11:72429600-72431400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr11:72429600-72431800	Enhancers	Psoas Muscle	Psoas
33	chr11:72429600-72432400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
34	chr11:72429800-72431400	Enhancers	Placenta	Placenta
35	chr11:72429800-72431800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:72429800-72431800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:72429800-72431800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
38	chr11:72429800-72431800	Enhancers	HSMMtube	muscle
39	chr11:72429800-72433200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr11:72429800-72434000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr11:72430000-72431400	Enhancers	Fetal Brain Female	brain
42	chr11:72430200-72431400	Genic enhancers	Dnd41	blood
43	chr11:72430200-72431600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:72430200-72431600	Genic enhancers	Fetal Stomach	stomach
45	chr11:72430200-72431800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr11:72430200-72431800	Enhancers	Gastric	stomach
47	chr11:72430200-72431800	Genic enhancers	NHLF	lung
48	chr11:72430200-72432600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr11:72430200-72434000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:72430400-72431400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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