Variant report

Variant	rs2146794
Chromosome Location	chr9:6989575-6989576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11795389	1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs1407856	1.00[YRI][hapmap]
rs16925051	0.82[AMR][1000 genomes]
rs16925220	1.00[YRI][hapmap]
rs17180316	1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs17505270	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2146793	0.85[AMR][1000 genomes]
rs2296067	0.80[AMR][1000 genomes]
rs2296068	0.80[AMR][1000 genomes]
rs2381527	0.82[AMR][1000 genomes]
rs2760646	0.81[AMR][1000 genomes]
rs73397850	0.83[AMR][1000 genomes]
rs73397861	0.83[AMR][1000 genomes]
rs73639442	0.81[AMR][1000 genomes]
rs7866711	1.00[YRI][hapmap]
rs818912	0.84[AMR][1000 genomes]
rs818913	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv466111	chr9:6567841-7017391	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv613208	chr9:6567841-7017391	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1024831	chr9:6573752-7018641	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
8	nsv613252	chr9:6715730-7022554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv1023461	chr9:6774993-7022554	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv831500	chr9:6847952-6992535	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv892185	chr9:6929053-7070962	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1021234	chr9:6933222-7015397	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv870178	chr9:6941584-7060029	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv892186	chr9:6942605-7075305	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv892187	chr9:6974101-7035727	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2146794	PDCD1LG2	cis	cerebellum	SCAN
rs2146794	KDM4C	cis	cerebellum	SCAN
rs2146794	CDC37L1	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6954200-6994800	Weak transcription	Gastric	stomach
2	chr9:6956000-6996000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:6972000-7013200	Weak transcription	Fetal Kidney	kidney
4	chr9:6974000-6995000	Weak transcription	HMEC	breast
5	chr9:6974200-6999800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:6975400-6997400	Weak transcription	Fetal Heart	heart
7	chr9:6976200-7011800	Weak transcription	Psoas Muscle	Psoas
8	chr9:6977000-7008200	Strong transcription	Primary B cells from cord blood	blood
9	chr9:6977600-6999200	Strong transcription	Primary T cells from cord blood	blood
10	chr9:6977800-7008200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr9:6978800-7008200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:6979000-6993600	Weak transcription	Esophagus	oesophagus
13	chr9:6979600-6997800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr9:6979600-6998200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr9:6979600-7008000	Weak transcription	NHEK	skin
16	chr9:6979800-7018600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr9:6980200-6998000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr9:6980200-7008400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr9:6980400-6992600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr9:6980600-6990000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr9:6980800-7004200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr9:6981000-6991000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:6981000-6997400	Strong transcription	Liver	Liver
24	chr9:6981000-6997800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:6981000-6998200	Strong transcription	Fetal Thymus	thymus
26	chr9:6981400-7008000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:6981400-7011200	Weak transcription	HUVEC	blood vessel
28	chr9:6981600-6997200	Weak transcription	HSMM	muscle
29	chr9:6981600-6999000	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr9:6982400-6989600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr9:6982400-6996200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:6982600-6997600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:6982600-6998800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:6982600-7000200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr9:6982600-7008200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:6982600-7008200	Weak transcription	NHLF	lung
37	chr9:6982800-6992000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:6982800-6993800	Weak transcription	Colonic Mucosa	Colon
39	chr9:6982800-7004200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr9:6983000-7008600	Weak transcription	Fetal Brain Female	brain
41	chr9:6983200-6992000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr9:6983400-7010200	Weak transcription	Stomach Mucosa	stomach
43	chr9:6983800-7008200	Weak transcription	A549	lung
44	chr9:6984000-6995200	Weak transcription	Fetal Brain Male	brain
45	chr9:6984000-7018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:6984200-6991600	Strong transcription	Placenta	Placenta
47	chr9:6985200-7007800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr9:6985200-7008200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:6985400-6995200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr9:6985600-6996800	Weak transcription	HSMMtube	muscle

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