Variant report

Variant	rs689749
Chromosome Location	chr9:98639447-98639448
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:98636530-98639513	GM12878	blood:	n/a	n/a
2	POLR2A	chr9:98637138-98639605	IMR90	lung:	n/a	n/a
3	POLR2A	chr9:98636881-98639571	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr9:98636554-98639599	K562	blood:	n/a	n/a
5	MEF2A	chr9:98638911-98639464	K562	blood:	n/a	chr9:98639184-98639199

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:98270649..98275167-chr9:98636318..98639773,5	MCF-7	breast:
2	chr9:98637191..98639517-chr9:98666345..98668961,2	MCF-7	breast:
3	chr9:98637084..98640693-chr9:98667295..98670393,4	K562	blood:
4	chr9:98638841..98641088-chr9:98696754..98699064,2	K562	blood:
5	chr9:98187335..98191305-chr9:98637767..98639481,3	MCF-7	breast:
6	chr5:131629322..131630937-chr9:98636920..98639534,2	MCF-7	breast:
7	chr17:56736371..56738298-chr9:98637681..98639486,2	MCF-7	breast:
8	chr9:98614433..98624477-chr9:98629889..98639636,23	MCF-7	breast:
9	chr9:98277796..98280674-chr9:98636940..98639822,3	K562	blood:
10	chr15:52121718..52122280-chr9:98639010..98639775,2	Hela-S3	cervix:
11	chr9:98636642..98639611-chr9:98680367..98683270,2	K562	blood:
12	chr9:98637678..98640109-chr9:98685155..98688009,2	K562	blood:
13	chr9:98188917..98190953-chr9:98637709..98639661,2	MCF-7	breast:

No data

Variant related genes	Relation type
LINC00476	TF binding region
ENSG00000199202	Chromatin interaction
ENSG00000237857	Chromatin interaction
ENSG00000252847	Chromatin interaction
ENSG00000182150	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000138594	Chromatin interaction
ENSG00000237631	Chromatin interaction
ENSG00000197208	Chromatin interaction
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10121403	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10481647	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10739632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760675	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760692	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10818017	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10983622	0.81[CHB][hapmap]
rs10983692	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10983739	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10983773	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10983818	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12004422	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12375861	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12553442	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1410783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1928253	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2117432	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2164156	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2164157	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs238	0.92[CEU][hapmap]
rs2770837	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3930253	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4743458	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs583716	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs585223	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs591579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs601916	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs615866	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs617884	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs626264	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs631273	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs636456	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs640281	0.83[AMR][1000 genomes]
rs643815	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478984	0.84[ASN][1000 genomes]
rs6479036	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs676453	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs678244	0.96[CEU][hapmap]
rs680468	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs680754	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs683829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs689627	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs689820	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689979	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs690222	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs690304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690335	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs690420	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs690455	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs690484	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs700963	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7024710	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7028281	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7868559	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7874897	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs816671	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs816676	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs816681	0.86[ASN][1000 genomes]
rs913408	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9409321	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9409322	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv524894	chr9:98637430-98640244	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs689749	LINC00476	cis	lung	GTEx
rs689749	LINC00476	cis	Artery Aorta	GTEx
rs689749	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs689749	LINC00476	cis	Adipose Subcutaneous	GTEx
rs689749	LINC00476	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98636400-98639600	Active TSS	H1 Cell Line	embryonic stem cell
2	chr9:98636400-98639600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:98636400-98639800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr9:98636600-98639800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:98636600-98639800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:98636600-98640000	Active TSS	A549	lung
7	chr9:98637000-98639600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:98637000-98639800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr9:98637000-98639800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr9:98637000-98640400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:98637200-98639800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:98637200-98639800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr9:98637200-98639800	Active TSS	Psoas Muscle	Psoas
14	chr9:98637200-98639800	Active TSS	K562	blood
15	chr9:98637200-98640400	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr9:98637200-98640400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:98637200-98640600	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr9:98637400-98639800	Active TSS	HMEC	breast
19	chr9:98638400-98639800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:98638400-98640000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr9:98638600-98639600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr9:98638600-98639600	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr9:98638600-98639600	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr9:98638600-98639800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr9:98638600-98639800	Flanking Active TSS	HUVEC	blood vessel
26	chr9:98638600-98640200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr9:98638600-98640400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:98638800-98639600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr9:98638800-98639600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr9:98638800-98639600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:98638800-98639600	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr9:98638800-98639600	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr9:98638800-98639600	Flanking Active TSS	Fetal Thymus	thymus
34	chr9:98638800-98639600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr9:98638800-98639600	Active TSS	HepG2	liver
36	chr9:98638800-98639800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr9:98638800-98639800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr9:98638800-98639800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr9:98638800-98639800	Flanking Active TSS	Osteobl	bone
40	chr9:98638800-98640000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:98638800-98640000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr9:98638800-98640000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:98638800-98640000	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr9:98638800-98640000	Flanking Active TSS	Fetal Lung	lung
45	chr9:98638800-98640000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr9:98638800-98640200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr9:98638800-98640400	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr9:98638800-98640600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr9:98638800-98640600	Flanking Active TSS	Dnd41	blood
50	chr9:98638800-98648000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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