Variant report

Variant	rs2781000
Chromosome Location	chr9:86280847-86280848
allele	C/T
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	chr9:86280767-86281323	HUVEC	blood vessel:	n/a	n/a
2	SPI1	chr9:86280461-86280899	HL-60	blood:	n/a	chr9:86280769-86280782
3	POLR2A	chr9:86280616-86281143	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr9:86280503-86280850	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
UBQLN1	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10115799	0.91[CEU][hapmap];0.81[CHB][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10119344	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10125432	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1035274	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1044175	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10746718	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs10746719	0.95[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10746720	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10746721	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10780621	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10868040	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10868044	0.90[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10868045	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11140209	0.82[CHB][hapmap]
rs1333863	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1333865	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1360685	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1413293	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1572135	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1889260	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1961952	0.80[EUR][1000 genomes]
rs1968216	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2042042	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2058912	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2542775	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2542776	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2542803	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2780969	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2780972	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2780975	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2780982	1.00[JPT][hapmap]
rs2780995	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2780997	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2780998	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2780999	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2781001	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2781003	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2811909	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2811912	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2811922	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2811923	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2811924	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2811925	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2811926	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2811927	0.95[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2811928	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2811929	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2811930	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2811931	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4146741	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4242623	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4877263	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4877798	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6559737	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6559739	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7023082	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7039019	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7469301	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7850944	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7865296	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7874980	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs944946	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs961807	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]

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

No data

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	chr9:86263400-86298800	Strong transcription	Fetal Thymus	thymus
6	chr9:86264600-86281400	Strong transcription	HSMMtube	muscle
7	chr9:86264600-86284200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:86264600-86284400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:86264600-86297000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr9:86264800-86281800	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:86264800-86294600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:86264800-86295600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:86264800-86298200	Strong transcription	Dnd41	blood
14	chr9:86264800-86300200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:86265000-86282000	Strong transcription	Placenta	Placenta
16	chr9:86265000-86284400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:86265000-86295200	Strong transcription	HSMM	muscle
18	chr9:86265000-86296800	Strong transcription	Liver	Liver
19	chr9:86265000-86298800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr9:86265200-86281400	Strong transcription	NH-A	brain
21	chr9:86265400-86285800	Weak transcription	Gastric	stomach
22	chr9:86266000-86281600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:86266000-86283600	Strong transcription	NHDF-Ad	bronchial
24	chr9:86266200-86296000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr9:86266400-86281800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:86266400-86298800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr9:86267000-86282200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:86267000-86292000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr9:86267000-86293800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr9:86267400-86296800	Strong transcription	A549	lung
31	chr9:86267400-86297800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:86267600-86282000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr9:86267600-86296800	Strong transcription	Primary hematopoietic stem cells	blood
34	chr9:86267800-86295400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr9:86268000-86282000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:86268000-86295400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr9:86268000-86298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:86268200-86294800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr9:86268400-86284000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr9:86268600-86281600	Strong transcription	Fetal Lung	lung
41	chr9:86269000-86294200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:86269200-86281200	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr9:86269200-86289000	Strong transcription	Osteobl	bone
44	chr9:86269200-86297800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:86269400-86298600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr9:86270200-86281600	Strong transcription	HMEC	breast
47	chr9:86270400-86295400	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr9:86270800-86281600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr9:86270800-86281800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
50	chr9:86270800-86298000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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