Variant report

Variant	rs2296961
Chromosome Location	chr10:97023630-97023631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:96989618..96991184-chr10:97021389..97024082,2	MCF-7	breast:
2	chr10:97022981..97025591-chr10:97038019..97040228,2	MCF-7	breast:
3	chr10:97023146..97026051-chr10:97049239..97052357,4	MCF-7	breast:
4	chr10:97023137..97024649-chr10:97048787..97050553,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000107438	Chromatin interaction
ENSG00000234026	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10786195	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs11188250	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11188255	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs11593722	1.00[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11594748	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12413028	0.85[MEX][hapmap]
rs12415795	0.85[MEX][hapmap]
rs12775067	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12776258	0.86[JPT][hapmap]
rs1385065	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17110556	1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1887182	0.86[JPT][hapmap]
rs35497513	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918905	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58140424	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2296961	HELLS	cis	cerebellum	SCAN
rs2296961	ZFYVE27	cis	cerebellum	SCAN
rs2296961	CYP2C8	cis	cerebellum	SCAN
rs2296961	PIPSL	cis	cerebellum	SCAN
rs2296961	LOXL4	cis	cerebellum	SCAN
rs2296961	PDLIM1	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96991000-97024000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr10:96998400-97030200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:97000400-97024400	Weak transcription	Fetal Kidney	kidney
4	chr10:97007000-97026400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr10:97009200-97028200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr10:97016400-97026200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr10:97016800-97036000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr10:97017200-97024400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr10:97018000-97024000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr10:97018800-97023800	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr10:97018800-97030000	Weak transcription	Thymus	Thymus
12	chr10:97019200-97024800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr10:97019400-97026400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr10:97019600-97024800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:97019800-97023800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr10:97020000-97024000	Genic enhancers	Left Ventricle	heart
17	chr10:97020000-97026600	Genic enhancers	Fetal Intestine Large	intestine
18	chr10:97020200-97024200	Genic enhancers	Lung	lung
19	chr10:97020200-97024600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
20	chr10:97020200-97025000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr10:97020200-97026600	Genic enhancers	Fetal Intestine Small	intestine
22	chr10:97020200-97026600	Enhancers	Right Atrium	heart
23	chr10:97020400-97024400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
24	chr10:97020400-97027000	Genic enhancers	HepG2	liver
25	chr10:97020800-97024400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr10:97021000-97026200	Weak transcription	Colon Smooth Muscle	Colon
27	chr10:97021000-97026600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr10:97021000-97034400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr10:97021200-97025200	Strong transcription	GM12878-XiMat	blood
30	chr10:97021200-97025400	Weak transcription	Fetal Lung	lung
31	chr10:97021200-97026000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr10:97021200-97026200	Weak transcription	HUVEC	blood vessel
33	chr10:97021200-97026600	Genic enhancers	NHEK	skin
34	chr10:97021400-97024000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr10:97021400-97024000	Weak transcription	Hela-S3	cervix
36	chr10:97021400-97024200	Genic enhancers	A549	lung
37	chr10:97021400-97024400	Strong transcription	Fetal Stomach	stomach
38	chr10:97021400-97025800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr10:97021400-97026000	Weak transcription	NH-A	brain
40	chr10:97021400-97026200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr10:97021400-97026200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr10:97021400-97036400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr10:97021600-97024200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr10:97021600-97024400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:97021600-97024600	Strong transcription	Colonic Mucosa	Colon
46	chr10:97021600-97027800	Weak transcription	HSMM	muscle
47	chr10:97021800-97023800	Strong transcription	Pancreas	Pancrea
48	chr10:97021800-97024000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr10:97021800-97024400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr10:97021800-97025600	Strong transcription	Liver	Liver

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