Variant report

Variant	rs2306609
Chromosome Location	chr11:72399607-72399608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:72399569-72400092	K562	blood:	n/a	n/a
2	POLR2A	chr11:72399371-72400391	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:72395838..72397835-chr11:72397897..72400604,2	MCF-7	breast:

Variant related genes	Relation type
ARAP1	TF binding region
ENSG00000256007	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11235557	0.82[EUR][1000 genomes]
rs11235558	0.91[EUR][1000 genomes]
rs11235559	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs12146545	0.87[CHB][hapmap]
rs12362256	0.81[ASN][1000 genomes]
rs12363065	0.86[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs12576046	0.93[ASN][1000 genomes]
rs12576058	0.87[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12786302	0.95[ASN][1000 genomes]
rs12787293	0.93[ASN][1000 genomes]
rs12797368	0.81[EUR][1000 genomes]
rs12797791	0.85[CHB][hapmap]
rs12799451	0.93[ASN][1000 genomes]
rs12802369	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12804316	0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs1391888	0.88[CEU][hapmap];0.87[CHB][hapmap]
rs163694	0.82[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1872126	0.87[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs189332	0.89[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2035467	0.89[CEU][hapmap];0.87[CHB][hapmap];0.82[EUR][1000 genomes]
rs341053	0.87[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs341060	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs341061	0.89[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs341062	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34142547	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs342322	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34285624	0.93[ASN][1000 genomes]
rs34802028	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35748558	0.93[ASN][1000 genomes]
rs3758934	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3758935	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3758936	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3781913	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3781916	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs458275	0.80[CHB][hapmap]
rs7126790	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs900613	1.00[CEU][hapmap];0.80[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs900614	1.00[CEU][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs900615	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs907857	0.81[EUR][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	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	nsv523601	chr11:72281884-72430935	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2306609	STARD10	cis	cerebellum	SCAN
rs2306609	KRTAP5-10	cis	parietal	SCAN
rs2306609	ARAP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72391400-72403800	Weak transcription	Small Intestine	intestine
2	chr11:72392200-72402600	Weak transcription	HUVEC	blood vessel
3	chr11:72392800-72404000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:72392800-72404800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:72392800-72405600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:72393200-72400800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:72393200-72403800	Weak transcription	Fetal Kidney	kidney
8	chr11:72393800-72413400	Strong transcription	Fetal Intestine Small	intestine
9	chr11:72393800-72423200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr11:72394000-72413800	Strong transcription	Fetal Intestine Large	intestine
11	chr11:72394000-72414600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:72394000-72426800	Strong transcription	Thymus	Thymus
13	chr11:72394200-72408000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:72394200-72423600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr11:72394200-72425800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr11:72394200-72429000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:72394400-72412000	Strong transcription	GM12878-XiMat	blood
18	chr11:72394400-72423200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:72394400-72423800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr11:72394400-72424400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr11:72394600-72400800	Genic enhancers	Stomach Smooth Muscle	stomach
22	chr11:72394600-72412800	Strong transcription	Gastric	stomach
23	chr11:72394600-72413200	Strong transcription	Lung	lung
24	chr11:72394600-72428800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:72394600-72429400	Strong transcription	Primary T cells from cord blood	blood
26	chr11:72394600-72430200	Strong transcription	Dnd41	blood
27	chr11:72395000-72401400	Genic enhancers	Placenta	Placenta
28	chr11:72395000-72408800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:72395000-72413600	Strong transcription	Fetal Brain Female	brain
30	chr11:72395000-72423800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:72395000-72429800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr11:72395200-72400400	Strong transcription	Liver	Liver
33	chr11:72395200-72402400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr11:72395200-72408400	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr11:72395200-72425600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr11:72395200-72429000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:72395400-72403800	Weak transcription	K562	blood
38	chr11:72395400-72414200	Strong transcription	Brain Angular Gyrus	brain
39	chr11:72395400-72414200	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr11:72395400-72414400	Strong transcription	Brain Germinal Matrix	brain
41	chr11:72395600-72399800	Weak transcription	Stomach Mucosa	stomach
42	chr11:72395600-72404600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:72395800-72414000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:72396000-72401400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:72396000-72402200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:72396000-72402600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr11:72396000-72403000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:72396000-72403600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr11:72396000-72405400	Strong transcription	Esophagus	oesophagus
50	chr11:72396000-72405600	Weak transcription	NH-A	brain

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