Variant report

Variant	rs10239787
Chromosome Location	chr7:27970153-27970154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27967354..27970328-chr7:27973178..27975197,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10244948	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10248465	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10250533	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10275982	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10278615	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10282662	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10951188	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12531234	0.87[ASW][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs13236531	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1557780	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs28507096	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35135622	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4722745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67583972	0.83[ASN][1000 genomes]
rs7787576	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7804500	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7804617	1.00[CHB][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs7805497	1.00[CHB][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1024819	chr7:27949955-28020969	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10239787	C7orf41	cis	cerebellum	SCAN
rs10239787	HOXA10	cis	cerebellum	SCAN
rs10239787	PRR15	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27941400-27990800	Weak transcription	Primary T cells from cord blood	blood
2	chr7:27942400-28005600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr7:27956600-27979800	Weak transcription	Aorta	Aorta
4	chr7:27957200-27979000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr7:27957600-28000800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:27957800-27973400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:27961000-27976000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:27961000-27983400	Weak transcription	NH-A	brain
9	chr7:27963400-27978000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:27963600-27970600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr7:27963600-27971800	Weak transcription	Fetal Stomach	stomach
12	chr7:27963600-27975600	Weak transcription	Fetal Heart	heart
13	chr7:27963600-27976400	Weak transcription	Psoas Muscle	Psoas
14	chr7:27963800-27975400	Weak transcription	Fetal Muscle Leg	muscle
15	chr7:27964000-27979200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:27964600-27972200	Weak transcription	NHDF-Ad	bronchial
17	chr7:27964600-27973200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:27964600-27975400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:27964800-27973200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:27966400-27976600	Weak transcription	Primary B cells from cord blood	blood
21	chr7:27966600-27975400	Weak transcription	Left Ventricle	heart
22	chr7:27967000-27971800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr7:27967800-27970800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:27968200-27973000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:27968400-27979000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr7:27968600-27971800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:27969000-27973400	Weak transcription	Brain Angular Gyrus	brain
28	chr7:27969200-27971800	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:27969200-27975400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr7:27969400-27972600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:27970000-27980000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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