Variant report

Variant	rs2781002
Chromosome Location	chr9:86279025-86279026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86277294..86279925-chr9:86313746..86316276,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10119441	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10121882	0.83[ASW][hapmap]
rs10124714	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10217326	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1044214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10481737	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1052690	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10868039	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11140214	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11140224	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11792478	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12335711	0.83[ASW][hapmap]
rs12340935	0.88[ASW][hapmap];0.82[YRI][hapmap]
rs12344615	0.83[ASW][hapmap]
rs12345514	0.83[ASW][hapmap]
rs12346707	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12351677	0.82[YRI][hapmap]
rs13301956	0.82[YRI][hapmap]
rs17421460	1.00[CHD][hapmap]
rs2068465	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2542804	0.85[ASN][1000 genomes]
rs2780970	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2780971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2780973	0.92[ASN][1000 genomes]
rs2780974	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2780976	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2780980	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2780994	0.85[ASN][1000 genomes]
rs2781004	0.92[ASN][1000 genomes]
rs2781005	0.92[ASN][1000 genomes]
rs2781006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2781008	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2811904	0.92[ASN][1000 genomes]
rs2811907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2811908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2811910	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2811911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2811913	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2811914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2811915	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2811917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2811918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs41308878	0.85[ASN][1000 genomes]
rs41309243	0.85[ASN][1000 genomes]
rs6559740	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7045761	0.83[ASW][hapmap]
rs72746868	0.85[ASN][1000 genomes]
rs72746869	0.85[ASN][1000 genomes]
rs72746871	0.85[ASN][1000 genomes]
rs72746879	0.85[ASN][1000 genomes]
rs72746880	0.85[ASN][1000 genomes]
rs72746882	0.85[ASN][1000 genomes]
rs7866941	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9410586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9410882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs944947	0.83[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2781002	UBQLN1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86244800-86285800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:86252800-86294000	Weak transcription	Small Intestine	intestine
3	chr9:86260600-86300400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:86260800-86281400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:86261000-86280200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:86263400-86298800	Strong transcription	Fetal Thymus	thymus
7	chr9:86264400-86280200	Strong transcription	Fetal Muscle Leg	muscle
8	chr9:86264600-86280200	Strong transcription	Adipose Nuclei	Adipose
9	chr9:86264600-86280400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr9:86264600-86280600	Strong transcription	Stomach Smooth Muscle	stomach
11	chr9:86264600-86281400	Strong transcription	HSMMtube	muscle
12	chr9:86264600-86284200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:86264600-86284400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:86264600-86297000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr9:86264800-86279400	Strong transcription	Primary T cells from cord blood	blood
16	chr9:86264800-86280200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr9:86264800-86280200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr9:86264800-86280200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr9:86264800-86281800	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:86264800-86294600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:86264800-86295600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:86264800-86298200	Strong transcription	Dnd41	blood
23	chr9:86264800-86300200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:86265000-86280000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr9:86265000-86280800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr9:86265000-86282000	Strong transcription	Placenta	Placenta
27	chr9:86265000-86284400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:86265000-86295200	Strong transcription	HSMM	muscle
29	chr9:86265000-86296800	Strong transcription	Liver	Liver
30	chr9:86265000-86298800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr9:86265200-86281400	Strong transcription	NH-A	brain
32	chr9:86265400-86285800	Weak transcription	Gastric	stomach
33	chr9:86266000-86281600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:86266000-86283600	Strong transcription	NHDF-Ad	bronchial
35	chr9:86266200-86280600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr9:86266200-86296000	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:86266400-86279800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr9:86266400-86281800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:86266400-86298800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr9:86267000-86282200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:86267000-86292000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr9:86267000-86293800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr9:86267400-86280600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr9:86267400-86296800	Strong transcription	A549	lung
45	chr9:86267400-86297800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr9:86267600-86280600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr9:86267600-86282000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr9:86267600-86296800	Strong transcription	Primary hematopoietic stem cells	blood
49	chr9:86267800-86279600	Strong transcription	Fetal Brain Female	brain
50	chr9:86267800-86295400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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