Variant report

Variant	rs4743417
Chromosome Location	chr9:98706016-98706017
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10988581	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10988792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988804	0.82[EUR][1000 genomes]
rs11790370	0.91[AFR][1000 genomes]
rs11790491	0.81[EUR][1000 genomes]
rs11794054	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12001	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12683310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12685221	0.91[AFR][1000 genomes]
rs12685318	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12685807	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16910298	0.81[EUR][1000 genomes]
rs16910418	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1831228	0.88[AFR][1000 genomes]
rs1999023	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2026032	0.82[EUR][1000 genomes]
rs2069053	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2274653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34533243	0.91[AFR][1000 genomes]
rs3780574	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs3802438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742775	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4742781	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4743391	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743400	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743418	0.98[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4743419	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73536517	0.82[EUR][1000 genomes]
rs7868270	0.81[EUR][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	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1035723	chr9:98701628-98734356	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4743417	LINC00476	cis	Whole Blood	GTEx
rs4743417	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx
rs4743417	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs4743417	LINC00476	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
3	chr9:98675400-98718600	Weak transcription	Esophagus	oesophagus
4	chr9:98677600-98709000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:98678800-98718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
7	chr9:98686400-98709000	Weak transcription	Right Ventricle	heart
8	chr9:98686400-98711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr9:98687800-98709000	Weak transcription	Lung	lung
11	chr9:98687800-98718400	Weak transcription	Stomach Mucosa	stomach
12	chr9:98687800-98726000	Weak transcription	Gastric	stomach
13	chr9:98690400-98707000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr9:98690600-98709800	Weak transcription	HMEC	breast
15	chr9:98694400-98706800	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr9:98694600-98708400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr9:98695600-98718200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr9:98695800-98709200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:98695800-98742400	Weak transcription	NHLF	lung
20	chr9:98696200-98709600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:98696400-98706600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr9:98697800-98707000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:98697800-98713200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:98698800-98709200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:98699200-98707000	Strong transcription	Fetal Thymus	thymus
26	chr9:98699400-98709000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:98699400-98709600	Weak transcription	Brain Substantia Nigra	brain
28	chr9:98699600-98708400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:98699600-98717600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr9:98699800-98718600	Weak transcription	NHEK	skin
31	chr9:98700600-98706800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr9:98700600-98707000	Strong transcription	Liver	Liver
33	chr9:98701000-98706800	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:98701200-98706800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr9:98701600-98706800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:98701600-98709000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:98702000-98706600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr9:98702000-98707000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr9:98702200-98706400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr9:98702200-98706600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr9:98702200-98706600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr9:98702200-98706800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:98702400-98706800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr9:98702400-98707000	Strong transcription	Fetal Intestine Large	intestine
45	chr9:98702400-98709200	Weak transcription	Fetal Stomach	stomach
46	chr9:98702400-98718600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:98702400-98718600	Weak transcription	Small Intestine	intestine
48	chr9:98702600-98706800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:98702600-98707000	Strong transcription	Primary B cells from cord blood	blood
50	chr9:98702600-98707800	Strong transcription	Primary monocytes fromperipheralblood	blood

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