Variant report

Variant	rs1000620
Chromosome Location	chr11:72509713-72509714
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr11:72509671-72509756	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:72509387-72509809	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr11:72509640-72509839	K562	blood:	n/a	n/a
4	POLR2A	chr11:72509065-72510187	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr11:72509541-72509743	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:72509209..72510815-chr11:72511215..72514128,2	MCF-7	breast:
2	chr11:72443164..72445322-chr11:72509462..72511840,2	MCF-7	breast:
3	chr11:72507503..72509715-chr11:72521788..72523914,2	MCF-7	breast:
4	chr11:72507542..72509877-chr11:72525232..72527170,2	MCF-7	breast:
5	chr11:72508865..72510632-chr11:72910076..72912141,2	MCF-7	breast:
6	chr11:72450505..72454170-chr11:72508930..72511524,3	MCF-7	breast:

No data

Variant related genes	Relation type
STARD10	TF binding region
ENSG00000168010	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10431171	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10431172	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10431174	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10751213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10751215	0.95[CEU][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10751216	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10898877	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898879	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898880	0.95[CEU][hapmap];0.88[CHD][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10898881	0.88[CHD][hapmap];0.80[JPT][hapmap]
rs11235592	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11235594	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11235596	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864653	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1975109	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35343925	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35668754	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35752694	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4459331	0.94[ASW][hapmap];0.95[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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4459332	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs485099	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944797	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944800	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944802	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944805	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs519790	0.86[YRI][hapmap]
rs6592486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6592489	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6592490	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs677231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7110719	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7952617	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	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	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
3	nsv825992	chr11:72476174-72524295	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1000620	ARHGEF17	cis	cerebellum	SCAN
rs1000620	FGF4	cis	cerebellum	SCAN
rs1000620	STARD10	cis	cerebellum	SCAN
rs1000620	STARD10	cis	Whole Blood	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72505600-72523600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr11:72505800-72519200	Weak transcription	GM12878-XiMat	blood
3	chr11:72505800-72519400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr11:72505800-72519800	Weak transcription	Fetal Intestine Small	intestine
5	chr11:72505800-72520200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:72505800-72523000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr11:72505800-72523600	Weak transcription	Stomach Mucosa	stomach
8	chr11:72506000-72509800	Weak transcription	Brain Germinal Matrix	brain
9	chr11:72506000-72516400	Weak transcription	Primary B cells from cord blood	blood
10	chr11:72506000-72518800	Weak transcription	Fetal Stomach	stomach
11	chr11:72506000-72519400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:72506000-72519400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:72506000-72519400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:72506000-72519400	Weak transcription	Brain Hippocampus Middle	brain
15	chr11:72506000-72519600	Weak transcription	HMEC	breast
16	chr11:72506000-72520000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:72506000-72520200	Weak transcription	Fetal Muscle Leg	muscle
18	chr11:72506000-72521800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:72506000-72522800	Weak transcription	Pancreas	Pancrea
20	chr11:72506000-72523200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:72506000-72523600	Weak transcription	Brain Angular Gyrus	brain
22	chr11:72506000-72523800	Weak transcription	Spleen	Spleen
23	chr11:72506200-72519400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:72506200-72523800	Weak transcription	Brain Anterior Caudate	brain
25	chr11:72506600-72518400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:72506600-72519200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:72506600-72519200	Weak transcription	Placenta	Placenta
28	chr11:72506600-72519400	Weak transcription	NH-A	brain
29	chr11:72506600-72519600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:72506600-72520200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:72506800-72518200	Weak transcription	Hela-S3	cervix
32	chr11:72508800-72510000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr11:72508800-72510000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr11:72508800-72510200	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr11:72508800-72510400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr11:72508800-72510600	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr11:72509000-72509800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr11:72509000-72509800	Enhancers	K562	blood
39	chr11:72509000-72510000	Enhancers	H9 Cell Line	embryonic stem cell
40	chr11:72509000-72510000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:72509000-72510000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:72509000-72510000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:72509000-72510000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:72509000-72510200	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr11:72509000-72510400	Enhancers	H1 Cell Line	embryonic stem cell
46	chr11:72509000-72510400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr11:72509000-72510400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr11:72509000-72510400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr11:72509000-72510600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:72509000-72510600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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